BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716850.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 768,010 number of mapped reads = 697,115 (90.77%) number of supplementary alignments = 3,658 (0.48%) number of secondary alignments = 0 number of mapped bases = 40,908,550 bp number of sequenced bases = 40,896,941 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,404 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2089 >>>>>>> ACTG content number of A's = 10,370,460 bp (25.36%) number of C's = 7,887,359 bp (19.29%) number of T's = 12,217,958 bp (29.87%) number of G's = 10,420,909 bp (25.48%) number of N's = 255 bp (0%) GC percentage = 44.77% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 213,438 number of insertions = 2,490 mapped reads with insertion percentage = 0.36% number of deletions = 7,362 mapped reads with deletion percentage = 1.05% homopolymer indels = 46.02% >>>>>>> Coverage mean coverageData = 0.0132X std coverageData = 0.1521X There is a 1.24% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% 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 4504406 0.018071794493141904 0.22824323538522873 chr2 243199373 3965728 0.01630648940858906 0.18605710834648628 chr3 198022430 2639364 0.013328611309335008 0.12046612648224998 chr4 191154276 1766918 0.009243413419640165 0.11725049440220606 chr5 180915260 2992569 0.016541274627690335 0.13474164735620717 chr6 171115067 1514238 0.008849238273097249 0.10513416649937053 chr7 159138663 2810645 0.017661609988516742 0.22289967891065626 chr8 146364022 1853630 0.012664519426775522 0.1424913928042222 chr9 141213431 1274267 0.009023695486869092 0.12125474819019644 chr10 135534747 1841675 0.013588212917828371 0.15888950769366444 chr11 135006516 1783248 0.013208606909017637 0.15034868738943186 chr12 133851895 1635878 0.012221552784142503 0.11642089725735785 chr13 115169878 1225776 0.01064319960467441 0.10817437214299158 chr14 107349540 890743 0.008297594940788754 0.09891118585235444 chr15 102531392 1801228 0.01756757579181213 0.13862874133479397 chr16 90354753 1184880 0.013113643285594506 0.12377279837148984 chr17 81195210 1544856 0.01902644256970331 0.15038822028203971 chr18 78077248 1348200 0.017267514346817142 0.24012730266349083 chr19 59128983 634243 0.010726431739913403 0.16407237970363014 chr20 63025520 1041736 0.01652879658906424 0.13628684605923186 chr21 48129895 528159 0.010973616293989422 0.11758797555857836 chr22 51304566 489395 0.009539014519682322 0.10224415728061102 chrMT 16571 9689 0.5846961559350673 0.829864988966832 chrX 155270560 1521360 0.009798122709160062 0.11066964140276676 chrY 59373566 105719 0.0017805735299779703 0.06729147000279027