BamQC report
-----------------------------------
>>>>>>> Input
bam file = zr3644_12.deduplicated.sorted.bam
outfile = zr3644_12/genome_results.txt
>>>>>>> Reference
number of bases = 563,985,803 bp
number of contigs = 29
>>>>>>> Globals
number of windows = 428
number of reads = 46,444,264
number of mapped reads = 46,444,264 (100%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 23,222,132
number of mapped paired reads (second in pair) = 23,222,132
number of mapped paired reads (both in pair) = 46,444,264
number of mapped paired reads (singletons) = 0
number of overlapping read pairs = 19,809,731
number of mapped bases = 4,889,980,362 bp
number of sequenced bases = 4,867,319,037 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 7,617,196
duplication rate = 14.69%
>>>>>>> Insert size
mean insert size = 158.8856
std insert size = 69.8732
median insert size = 137
>>>>>>> Mapping quality
mean mapping quality = 23.1701
>>>>>>> ACTG content
number of A's = 2,008,969,581 bp (41.27%)
number of C's = 417,929,034 bp (8.59%)
number of T's = 2,028,721,724 bp (41.68%)
number of G's = 411,665,484 bp (8.46%)
number of N's = 33,214 bp (0%)
GC percentage = 17.04%
>>>>>>> Mismatches and indels
general error rate = 0.1956
number of mismatches = 927,266,514
number of insertions = 10,987,036
mapped reads with insertion percentage = 17.84%
number of deletions = 9,705,964
mapped reads with deletion percentage = 17.23%
homopolymer indels = 48.92%
>>>>>>> Coverage
mean coverageData = 8.6704X
std coverageData = 9.7745X
paired-end adapted mean coverage = 6.1388X
There is a 84.29% of reference with a coverageData >= 1X
There is a 78.31% of reference with a coverageData >= 2X
There is a 71.93% of reference with a coverageData >= 3X
There is a 66.4% of reference with a coverageData >= 4X
There is a 60.76% of reference with a coverageData >= 5X
There is a 55.42% of reference with a coverageData >= 6X
There is a 50.17% of reference with a coverageData >= 7X
There is a 45.18% of reference with a coverageData >= 8X
There is a 40.43% of reference with a coverageData >= 9X
There is a 35.99% of reference with a coverageData >= 10X
There is a 31.86% of reference with a coverageData >= 11X
There is a 28.09% of reference with a coverageData >= 12X
There is a 24.66% of reference with a coverageData >= 13X
There is a 21.57% of reference with a coverageData >= 14X
There is a 18.82% of reference with a coverageData >= 15X
There is a 16.38% of reference with a coverageData >= 16X
There is a 14.24% of reference with a coverageData >= 17X
There is a 12.37% of reference with a coverageData >= 18X
There is a 10.75% of reference with a coverageData >= 19X
There is a 9.35% of reference with a coverageData >= 20X
There is a 8.15% of reference with a coverageData >= 21X
There is a 7.11% of reference with a coverageData >= 22X
There is a 6.21% of reference with a coverageData >= 23X
There is a 5.45% of reference with a coverageData >= 24X
There is a 4.8% of reference with a coverageData >= 25X
There is a 4.24% of reference with a coverageData >= 26X
There is a 3.76% of reference with a coverageData >= 27X
There is a 3.36% of reference with a coverageData >= 28X
There is a 3% of reference with a coverageData >= 29X
There is a 2.7% of reference with a coverageData >= 30X
There is a 2.44% of reference with a coverageData >= 31X
There is a 2.21% of reference with a coverageData >= 32X
There is a 2.01% of reference with a coverageData >= 33X
There is a 1.83% of reference with a coverageData >= 34X
There is a 1.68% of reference with a coverageData >= 35X
There is a 1.54% of reference with a coverageData >= 36X
There is a 1.42% of reference with a coverageData >= 37X
There is a 1.31% of reference with a coverageData >= 38X
There is a 1.21% of reference with a coverageData >= 39X
There is a 1.13% of reference with a coverageData >= 40X
There is a 1.05% of reference with a coverageData >= 41X
There is a 0.98% of reference with a coverageData >= 42X
There is a 0.91% of reference with a coverageData >= 43X
There is a 0.85% of reference with a coverageData >= 44X
There is a 0.8% of reference with a coverageData >= 45X
There is a 0.74% of reference with a coverageData >= 46X
There is a 0.7% of reference with a coverageData >= 47X
There is a 0.66% of reference with a coverageData >= 48X
There is a 0.62% of reference with a coverageData >= 49X
There is a 0.58% of reference with a coverageData >= 50X
There is a 0.55% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
NC_088853.1 76070991 549388324 7.222047679121204 11.540007447638404
NC_088854.1 61469542 585833824 9.530473222006437 9.145052503550804
NC_088855.1 61039741 587305930 9.62169760844824 8.961276091819236
NC_088856.1 57946171 462434732 7.98041913761653 9.773757467852887
NC_088857.1 57274926 538597922 9.403729687926615 9.156332812763818
NC_088858.1 56905015 546688743 9.607039783751924 9.076736677381222
NC_088859.1 53672946 528518487 9.847018402902647 10.258475756165108
NC_088860.1 51133819 445270107 8.707937637124267 9.495736694584348
NC_088861.1 50364239 349198971 6.933470611955439 9.20780059284223
NC_088862.1 37310742 293567811 7.868184744221919 9.656716616601603
NW_027062568.1 15579 102608 6.5863020733038065 5.081563574502309
NW_027062569.1 16498 117392 7.115529155049097 13.547604925290116
NW_027062570.1 4000 31953 7.98825 8.564370660620662
NW_027062571.1 36893 21598 0.5854227089149703 2.133809302611635
NW_027062572.1 51000 58947 1.1558235294117647 4.091077182229311
NW_027062573.1 2000 29138 14.569 10.136797077972904
NW_027062574.1 37061 2602 0.07020857505194139 0.3485502755602434
NW_027062575.1 49428 295911 5.986707938820102 9.194846225043172
NW_027062576.1 49232 182483 3.7065932726681834 6.52383793922883
NW_027062577.1 17087 122477 7.167846901152923 6.084133532973186
NW_027062578.1 34507 318750 9.237256208885153 6.634137044490259
NW_027062579.1 64000 530317 8.286203125 10.912091476828888
NW_027062580.1 24229 145476 6.004209831194023 7.544700721982947
NW_027062581.1 5000 36123 7.2246 10.021093415391356
NW_027062582.1 18808 149103 7.927637175669927 8.302099628084612
NW_027062583.1 1000 230 0.23 0.4417012565071555
NW_027062584.1 74000 15961 0.2156891891891892 0.7378748984603963
NW_027062585.1 39334 261459 6.647150048304266 8.214969737390115
NW_027062586.1 258015 752983 2.9183690870685814 6.579947154648135