BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173944.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,928,160 number of mapped reads = 3,839,980 (97.76%) number of supplementary alignments = 484,245 (12.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,923,802 number of mapped paired reads (second in pair) = 1,916,178 number of mapped paired reads (both in pair) = 3,787,704 number of mapped paired reads (singletons) = 52,276 number of mapped bases = 428,277,981 bp number of sequenced bases = 427,930,099 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,012,657 duplication rate = 63.82% >>>>>>> Insert size mean insert size = 988,779.8189 std insert size = 8,853,713.7651 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 52.6944 >>>>>>> ACTG content number of A's = 128,500,474 bp (30.03%) number of C's = 84,365,844 bp (19.71%) number of T's = 127,445,877 bp (29.78%) number of G's = 87,614,703 bp (20.47%) number of N's = 3,201 bp (0%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 3,694,632 number of insertions = 47,640 mapped reads with insertion percentage = 1.19% number of deletions = 149,233 mapped reads with deletion percentage = 3.79% homopolymer indels = 40.28% >>>>>>> Coverage mean coverageData = 0.1383X std coverageData = 2.6977X There is a 3.08% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 1.64% of reference with a coverageData >= 3X There is a 1.33% of reference with a coverageData >= 4X There is a 0.97% of reference with a coverageData >= 5X There is a 0.83% of reference with a coverageData >= 6X There is a 0.61% of reference with a coverageData >= 7X There is a 0.54% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 34836895 0.13976653241718504 1.3456932738821423 chr2 243199373 36760374 0.15115324331037647 8.561975732580892 chr3 198022430 29714335 0.15005540028975506 1.1623431178298087 chr4 191154276 28702369 0.15015290058172698 1.4705994117299994 chr5 180915260 28034856 0.15496125644680278 1.18564029296836 chr6 171115067 25362849 0.14822101551115893 1.2385870856591727 chr7 159138663 24995545 0.15706770767578965 1.4355455818828542 chr8 146364022 21869373 0.14941768271440367 1.650646269458255 chr9 141213431 18542130 0.13130571128181143 1.2977580507609414 chr10 135534747 20595697 0.15195879621924555 1.7851286813115832 chr11 135006516 18774923 0.13906679141323816 1.1359523026134268 chr12 133851895 19298153 0.14417541865955652 1.1604519572756387 chr13 115169878 14855914 0.12899131489919613 1.086314504149667 chr14 107349540 13225317 0.12319863690147159 1.0716630441836539 chr15 102531392 12930325 0.12611088904362092 1.070081766750895 chr16 90354753 12534537 0.13872581777740015 1.2801202130059564 chr17 81195210 11608894 0.1429751089996565 1.1502664710121253 chr18 78077248 11867322 0.15199462460562135 1.513395293677371 chr19 59128983 7937346 0.13423782377586302 1.1706228418186424 chr20 63025520 9068992 0.1438939654920737 1.1507847104857256 chr21 48129895 6328018 0.13147790993518685 1.2805237528962496 chr22 51304566 5262458 0.10257289770271129 1.0661888729319946 chrMT 16571 408252 24.636533703457847 24.10243703274403 chrX 155270560 11367462 0.07321067174614428 0.7957159627812724 chrY 59373566 3395645 0.05719119178389925 1.0713341229974884