BamQC report
-----------------------------------
>>>>>>> Input
bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-220_S32_L004_dedup.sorted.bam
outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-220_S32_L004_dedup.sorted_stats/genome_results.txt
>>>>>>> Reference
number of bases = 942,353,201 bp
number of contigs = 18
>>>>>>> Globals
number of windows = 417
number of reads = 10,406,202
number of mapped reads = 10,406,202 (100%)
number of mapped paired reads (first in pair) = 5,203,101
number of mapped paired reads (second in pair) = 5,203,101
number of mapped paired reads (both in pair) = 10,406,202
number of mapped paired reads (singletons) = 0
number of mapped bases = 942,629,434 bp
number of sequenced bases = 937,487,580 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 3,122,494
duplication rate = 25.06%
>>>>>>> Insert size
mean insert size = 164.1957
std insert size = 95.7663
median insert size = 132
>>>>>>> Mapping quality
mean mapping quality = 19.3246
>>>>>>> ACTG content
number of A's = 356,201,067 bp (38%)
number of C's = 114,208,645 bp (12.18%)
number of T's = 354,666,646 bp (37.83%)
number of G's = 112,411,222 bp (11.99%)
number of N's = 60,093 bp (0.01%)
GC percentage = 24.17%
>>>>>>> Mismatches and indels
general error rate = 0.2148
number of mismatches = 188,519,644
number of insertions = 4,082,483
mapped reads with insertion percentage = 22.72%
number of deletions = 2,468,319
mapped reads with deletion percentage = 17.95%
homopolymer indels = 39.14%
>>>>>>> Coverage
mean coverageData = 1.0003X
std coverageData = 8.4696X
There is a 30.13% of reference with a coverageData >= 1X
There is a 18.33% of reference with a coverageData >= 2X
There is a 10.58% of reference with a coverageData >= 3X
There is a 7.24% of reference with a coverageData >= 4X
There is a 4.86% of reference with a coverageData >= 5X
There is a 3.57% of reference with a coverageData >= 6X
There is a 2.63% of reference with a coverageData >= 7X
There is a 2.05% of reference with a coverageData >= 8X
There is a 1.61% of reference with a coverageData >= 9X
There is a 1.31% of reference with a coverageData >= 10X
There is a 1.08% of reference with a coverageData >= 11X
There is a 0.92% of reference with a coverageData >= 12X
There is a 0.79% of reference with a coverageData >= 13X
There is a 0.69% of reference with a coverageData >= 14X
There is a 0.6% of reference with a coverageData >= 15X
There is a 0.54% of reference with a coverageData >= 16X
There is a 0.48% of reference with a coverageData >= 17X
There is a 0.44% of reference with a coverageData >= 18X
There is a 0.4% of reference with a coverageData >= 19X
There is a 0.36% of reference with a coverageData >= 20X
There is a 0.33% of reference with a coverageData >= 21X
There is a 0.31% of reference with a coverageData >= 22X
There is a 0.29% of reference with a coverageData >= 23X
There is a 0.27% of reference with a coverageData >= 24X
There is a 0.25% of reference with a coverageData >= 25X
There is a 0.23% of reference with a coverageData >= 26X
There is a 0.22% of reference with a coverageData >= 27X
There is a 0.21% of reference with a coverageData >= 28X
There is a 0.2% of reference with a coverageData >= 29X
There is a 0.18% of reference with a coverageData >= 30X
There is a 0.18% of reference with a coverageData >= 31X
There is a 0.17% of reference with a coverageData >= 32X
There is a 0.16% of reference with a coverageData >= 33X
There is a 0.15% of reference with a coverageData >= 34X
There is a 0.14% of reference with a coverageData >= 35X
There is a 0.14% of reference with a coverageData >= 36X
There is a 0.13% of reference with a coverageData >= 37X
There is a 0.13% of reference with a coverageData >= 38X
There is a 0.12% of reference with a coverageData >= 39X
There is a 0.11% of reference with a coverageData >= 40X
There is a 0.11% of reference with a coverageData >= 41X
There is a 0.11% of reference with a coverageData >= 42X
There is a 0.1% of reference with a coverageData >= 43X
There is a 0.1% of reference with a coverageData >= 44X
There is a 0.09% of reference with a coverageData >= 45X
There is a 0.09% of reference with a coverageData >= 46X
There is a 0.09% of reference with a coverageData >= 47X
There is a 0.08% of reference with a coverageData >= 48X
There is a 0.08% of reference with a coverageData >= 49X
There is a 0.08% of reference with a coverageData >= 50X
There is a 0.08% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
PGA_scaffold1__77_contigs__length_89643857 89643857 90772537 1.0125907121555469 4.220959063647581
PGA_scaffold2__36_contigs__length_69596280 69596280 73247137 1.0524576457247428 5.259293392352748
PGA_scaffold3__111_contigs__length_57743597 57743597 58929030 1.020529254524965 4.237712049579304
PGA_scaffold4__129_contigs__length_65288255 65288255 64656159 0.9903183811544665 10.278317253127161
PGA_scaffold5__109_contigs__length_67248332 67248332 59906055 0.8908184518242028 5.24133957927125
PGA_scaffold6__104_contigs__length_61759565 61759565 58670631 0.9499845246643172 6.960360579670406
PGA_scaffold7__69_contigs__length_43120122 43120122 41984159 0.9736558491184232 4.044181940598813
PGA_scaffold8__63_contigs__length_61151155 61151155 60033092 0.9817164042118256 4.173400081133774
PGA_scaffold9__45_contigs__length_38581958 38581958 45012577 1.1666742522502358 13.852141411224293
PGA_scaffold10__49_contigs__length_53961475 53961475 50014896 0.9268630258902301 4.724916096713111
PGA_scaffold11__79_contigs__length_51449921 51449921 45015247 0.8749332579150122 4.882377727179956
PGA_scaffold12__71_contigs__length_50438331 50438331 53047475 1.0517293881115932 6.156591479788271
PGA_scaffold13__52_contigs__length_44396874 44396874 43700117 0.9843061698443003 5.013312018665663
PGA_scaffold14__91_contigs__length_45393038 45393038 59044733 1.3007442462872831 22.9320536849055
PGA_scaffold15__101_contigs__length_47938513 47938513 39807183 0.830380011995783 3.9465800264574087
PGA_scaffold16__33_contigs__length_31980953 31980953 36208232 1.132181145446166 16.97958916124877
PGA_scaffold17__51_contigs__length_34923512 34923512 35978612 1.030211738155086 5.74339351235195
PGA_scaffold18__69_contigs__length_27737463 27737463 26601562 0.9590481292395054 7.760588019931985