BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16362018.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 303,936,886 number of mapped reads = 293,958,191 (96.72%) number of supplementary alignments = 13,160,330 (4.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 147,997,183 number of mapped paired reads (second in pair) = 145,961,008 number of mapped paired reads (both in pair) = 291,298,238 number of mapped paired reads (singletons) = 2,659,953 number of mapped bases = 40,877,695,812 bp number of sequenced bases = 40,842,861,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,522,469 duplication rate = 32.04% >>>>>>> Insert size mean insert size = 155,389.4478 std insert size = 3,821,711.5271 median insert size = 249 >>>>>>> Mapping quality mean mapping quality = 53.7844 >>>>>>> ACTG content number of A's = 11,810,974,344 bp (28.92%) number of C's = 8,583,087,231 bp (21.01%) number of T's = 11,749,840,872 bp (28.77%) number of G's = 8,695,867,289 bp (21.29%) number of N's = 3,091,303 bp (0.01%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 360,691,581 number of insertions = 7,236,242 mapped reads with insertion percentage = 2.34% number of deletions = 19,067,953 mapped reads with deletion percentage = 6.22% homopolymer indels = 44.81% >>>>>>> Coverage mean coverageData = 13.2047X std coverageData = 124.6877X There is a 91.4% of reference with a coverageData >= 1X There is a 91.06% of reference with a coverageData >= 2X There is a 90.42% of reference with a coverageData >= 3X There is a 89.33% of reference with a coverageData >= 4X There is a 87.59% of reference with a coverageData >= 5X There is a 85.09% of reference with a coverageData >= 6X There is a 81.75% of reference with a coverageData >= 7X There is a 77.58% of reference with a coverageData >= 8X There is a 72.68% of reference with a coverageData >= 9X There is a 67.17% of reference with a coverageData >= 10X There is a 61.24% of reference with a coverageData >= 11X There is a 55.09% of reference with a coverageData >= 12X There is a 48.91% of reference with a coverageData >= 13X There is a 42.88% of reference with a coverageData >= 14X There is a 37.14% of reference with a coverageData >= 15X There is a 31.8% of reference with a coverageData >= 16X There is a 26.94% of reference with a coverageData >= 17X There is a 22.59% of reference with a coverageData >= 18X There is a 18.76% of reference with a coverageData >= 19X There is a 15.44% of reference with a coverageData >= 20X There is a 12.62% of reference with a coverageData >= 21X There is a 10.23% of reference with a coverageData >= 22X There is a 8.25% of reference with a coverageData >= 23X There is a 6.62% of reference with a coverageData >= 24X There is a 5.29% of reference with a coverageData >= 25X There is a 4.21% of reference with a coverageData >= 26X There is a 3.35% of reference with a coverageData >= 27X There is a 2.66% of reference with a coverageData >= 28X There is a 2.12% of reference with a coverageData >= 29X There is a 1.7% of reference with a coverageData >= 30X There is a 1.36% of reference with a coverageData >= 31X There is a 1.1% of reference with a coverageData >= 32X There is a 0.9% of reference with a coverageData >= 33X There is a 0.75% of reference with a coverageData >= 34X There is a 0.62% of reference with a coverageData >= 35X There is a 0.53% of reference with a coverageData >= 36X There is a 0.46% of reference with a coverageData >= 37X There is a 0.4% of reference with a coverageData >= 38X There is a 0.35% of reference with a coverageData >= 39X There is a 0.32% of reference with a coverageData >= 40X There is a 0.29% of reference with a coverageData >= 41X There is a 0.27% of reference with a coverageData >= 42X There is a 0.25% of reference with a coverageData >= 43X There is a 0.23% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3337103829 13.38854770195337 279.83261701773745 chr2 243199373 3463044000 14.239526842859089 93.1775437021589 chr3 198022430 2685177736 13.559967605689922 12.411719219619027 chr4 191154276 2670166888 13.968648485791654 122.39350783020028 chr5 180915260 2447555878 13.528742008827779 10.319914460426144 chr6 171115067 2314613278 13.526647995293132 29.25556647314133 chr7 159138663 2205154316 13.856810623072786 85.4430757067543 chr8 146364022 2009412520 13.728869243563148 169.18452014110355 chr9 141213431 1748430283 12.381472998839607 139.01209500565363 chr10 135534747 2056160977 15.170729444014825 225.7897335922443 chr11 135006516 1839812274 13.627581308742165 57.08308016091968 chr12 133851895 1816526421 13.571167005144007 8.864214466912928 chr13 115169878 1276478491 11.083440506900597 8.249350758836538 chr14 107349540 1222025569 11.383612533411881 11.063247342069582 chr15 102531392 1138709552 11.105960133653506 8.427713899129744 chr16 90354753 1329395134 14.71306256572911 125.07480334468937 chr17 81195210 1146785955 14.123812907189969 70.94087458182392 chr18 78077248 1099898625 14.087312926295763 134.55339379459528 chr19 59128983 828853941 14.017726991854401 170.5036758119913 chr20 63025520 841357550 13.349474149519116 35.57608191493229 chr21 48129895 552494871 11.479245300659809 57.964261756056295 chr22 51304566 489582678 9.542672634634508 11.800132994410893 chrMT 16571 151059986 9115.924567014665 1459.1880988635132 chrX 155270560 2078937149 13.389126367548362 28.721611151317003 chrY 59373566 128957911 2.1719751682086943 143.45923978511118