BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617596.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 52,011,210 number of mapped reads = 50,216,889 (96.55%) number of supplementary alignments = 928,006 (1.78%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 25,369,951 number of mapped paired reads (second in pair) = 24,846,938 number of mapped paired reads (both in pair) = 49,466,744 number of mapped paired reads (singletons) = 750,145 number of mapped bases = 6,732,915,890 bp number of sequenced bases = 6,728,404,211 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,075,851 duplication rate = 24.26% >>>>>>> Insert size mean insert size = 120,695.1181 std insert size = 3,332,470.1922 median insert size = 283 >>>>>>> Mapping quality mean mapping quality = 53.5734 >>>>>>> ACTG content number of A's = 1,951,722,217 bp (29.01%) number of C's = 1,273,087,334 bp (18.92%) number of T's = 2,014,520,084 bp (29.94%) number of G's = 1,488,794,390 bp (22.13%) number of N's = 280,186 bp (0%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 73,274,659 number of insertions = 1,112,765 mapped reads with insertion percentage = 2.07% number of deletions = 2,265,759 mapped reads with deletion percentage = 4.33% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 2.1749X std coverageData = 22.5961X There is a 47.67% of reference with a coverageData >= 1X There is a 34.8% of reference with a coverageData >= 2X There is a 25.76% of reference with a coverageData >= 3X There is a 19.68% of reference with a coverageData >= 4X There is a 15.17% of reference with a coverageData >= 5X There is a 11.87% of reference with a coverageData >= 6X There is a 9.35% of reference with a coverageData >= 7X There is a 7.45% of reference with a coverageData >= 8X There is a 5.97% of reference with a coverageData >= 9X There is a 4.82% of reference with a coverageData >= 10X There is a 3.92% of reference with a coverageData >= 11X There is a 3.2% of reference with a coverageData >= 12X There is a 2.63% of reference with a coverageData >= 13X There is a 2.17% of reference with a coverageData >= 14X There is a 1.8% of reference with a coverageData >= 15X There is a 1.5% of reference with a coverageData >= 16X There is a 1.26% of reference with a coverageData >= 17X There is a 1.06% of reference with a coverageData >= 18X There is a 0.89% of reference with a coverageData >= 19X There is a 0.76% of reference with a coverageData >= 20X There is a 0.64% of reference with a coverageData >= 21X There is a 0.55% of reference with a coverageData >= 22X There is a 0.47% of reference with a coverageData >= 23X There is a 0.41% of reference with a coverageData >= 24X There is a 0.35% of reference with a coverageData >= 25X There is a 0.3% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.23% 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 0.16% 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 0.11% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 512700835 2.0569691379023687 23.31287708731178 chr2 243199373 603106110 2.4798834904890974 29.03503948283703 chr3 198022430 419542675 2.1186623909220788 3.860268425918089 chr4 191154276 427205582 2.234873270635076 16.58893856561073 chr5 180915260 390940985 2.1609066310934746 4.383852577156679 chr6 171115067 557345833 3.2571406058590973 31.217726121335332 chr7 159138663 348206282 2.188068414273406 24.365748183971498 chr8 146364022 324448307 2.216721722774194 7.086740599631618 chr9 141213431 299867115 2.123502792025498 46.84125820871418 chr10 135534747 347499869 2.563917199771657 39.60196249936459 chr11 135006516 284493988 2.107261163601911 17.65208219294463 chr12 133851895 298535295 2.230340444563747 7.90533042276421 chr13 115169878 206905587 1.796525190380075 3.5631652433225414 chr14 107349540 202454093 1.8859334935203262 4.44846665219633 chr15 102531392 187001121 1.82384260422408 4.655579115636603 chr16 90354753 210378210 2.3283579780246866 26.702531678423767 chr17 81195210 152452677 1.8776067824690643 34.208314050691776 chr18 78077248 278105519 3.561927784647328 37.083657687676464 chr19 59128983 87262233 1.4757945862184032 13.077878578731566 chr20 63025520 142343105 2.2584994935384906 6.127202709471159 chr21 48129895 87212624 1.812026059894791 8.865266814302194 chr22 51304566 63852628 1.2445798294054373 3.684659981722297 chrMT 16571 1400816 84.5341862289542 51.615303593531905 chrX 155270560 239716901 1.5438657592269907 6.625126855256658 chrY 59373566 59937500 1.0094980651827448 26.737959817884636