BamQC report ----------------------------------- >>>>>>> Input bam file = CF02-CM02-Zygote.deduplicated.sorted.bam outfile = CF02-CM02-Zygote/genome_results.txt >>>>>>> Reference number of bases = 684,741,128 bp number of contigs = 11 >>>>>>> Globals number of windows = 410 number of reads = 6,565,986 number of mapped reads = 6,565,986 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,282,993 number of mapped paired reads (second in pair) = 3,282,993 number of mapped paired reads (both in pair) = 6,565,986 number of mapped paired reads (singletons) = 0 number of overlapping read pairs = 3,278,341 number of mapped bases = 590,903,534 bp number of sequenced bases = 589,841,617 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,410,088 duplication rate = 41.11% >>>>>>> Insert size mean insert size = 93.0411 std insert size = 38.2272 median insert size = 87 >>>>>>> Mapping quality mean mapping quality = 13.6864 >>>>>>> ACTG content number of A's = 238,697,109 bp (40.47%) number of C's = 55,223,739 bp (9.36%) number of T's = 241,599,242 bp (40.96%) number of G's = 54,318,289 bp (9.21%) number of N's = 3,238 bp (0%) GC percentage = 18.57% >>>>>>> Mismatches and indels general error rate = 0.1444 number of mismatches = 84,598,451 number of insertions = 522,751 mapped reads with insertion percentage = 7.7% number of deletions = 786,461 mapped reads with deletion percentage = 11.48% homopolymer indels = 44.73% >>>>>>> Coverage mean coverageData = 0.863X std coverageData = 3.316X paired-end adapted mean coverage = 0.4453X There is a 20.63% of reference with a coverageData >= 1X There is a 19.75% of reference with a coverageData >= 2X There is a 8.35% of reference with a coverageData >= 3X There is a 7.91% of reference with a coverageData >= 4X There is a 4.31% of reference with a coverageData >= 5X There is a 4.07% of reference with a coverageData >= 6X There is a 2.57% of reference with a coverageData >= 7X There is a 2.43% of reference with a coverageData >= 8X There is a 1.69% of reference with a coverageData >= 9X There is a 1.6% of reference with a coverageData >= 10X There is a 1.18% of reference with a coverageData >= 11X There is a 1.12% of reference with a coverageData >= 12X There is a 0.87% of reference with a coverageData >= 13X There is a 0.83% of reference with a coverageData >= 14X There is a 0.66% of reference with a coverageData >= 15X There is a 0.63% of reference with a coverageData >= 16X There is a 0.52% of reference with a coverageData >= 17X There is a 0.5% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.4% of reference with a coverageData >= 20X There is a 0.34% of reference with a coverageData >= 21X There is a 0.33% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.15% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_035780.1 65668440 64290067 0.9790101150567914 3.3370752240393 NC_035781.1 61752955 65690499 1.063762843413728 3.3790346167699608 NC_035782.1 77061148 76763476 0.9961371974370276 3.4483367735615578 NC_035783.1 59691872 64420494 1.0792171838738782 3.4950377396347325 NC_035784.1 98698416 110455912 1.1191254781637023 3.5877295501721087 NC_035785.1 51258098 32812140 0.6401357303581573 2.7725422380273343 NC_035786.1 57830854 37518210 0.6487576683546814 2.8298504966420777 NC_035787.1 75944018 48905423 0.6439667571973872 2.706207644987076 NC_035788.1 104168038 67342652 0.6464809484076104 2.724344319923975 NC_035789.1 32650045 20318948 0.6223252678518514 2.5715272758923895 NC_007175.2 17244 2385713 138.3503247506379 156.1746473845296