BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716917.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 = 670,223 number of mapped reads = 594,535 (88.71%) number of supplementary alignments = 1,372 (0.2%) number of secondary alignments = 0 number of mapped bases = 33,567,713 bp number of sequenced bases = 33,557,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,614 duplication rate = 1.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5734 >>>>>>> ACTG content number of A's = 7,999,987 bp (23.84%) number of C's = 6,047,557 bp (18.02%) number of T's = 11,063,681 bp (32.97%) number of G's = 8,445,882 bp (25.17%) number of N's = 392 bp (0%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 172,685 number of insertions = 1,991 mapped reads with insertion percentage = 0.33% number of deletions = 6,378 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.29% >>>>>>> Coverage mean coverageData = 0.0108X std coverageData = 0.131X There is a 1.03% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 4000560 0.0160503511844811 0.18338416855825065 chr2 243199373 2858921 0.01175546205047165 0.17160944212064083 chr3 198022430 2150226 0.010858497191454524 0.10951367513989321 chr4 191154276 1493610 0.007813636353078494 0.0941694534144877 chr5 180915260 2447792 0.013530047161306348 0.1205099546471106 chr6 171115067 1309527 0.007652902943958757 0.09835872135247332 chr7 159138663 2294971 0.014421203224511193 0.19238335649714788 chr8 146364022 1502408 0.010264872333174883 0.11466774266712738 chr9 141213431 953304 0.006750802620184195 0.10289450717712605 chr10 135534747 1584643 0.011691784100205684 0.14336297930197056 chr11 135006516 1476210 0.010934361123725317 0.12680064272395808 chr12 133851895 1225278 0.00915398321405909 0.10031859981167487 chr13 115169878 1020843 0.008863802043794819 0.09769309246052776 chr14 107349540 756454 0.007046644075046805 0.08899363288700941 chr15 102531392 1493140 0.014562759471752807 0.12582758471331384 chr16 90354753 1009352 0.01117098953278086 0.11812709218915209 chr17 81195210 1257772 0.01549071675533569 0.1329065282493741 chr18 78077248 1107351 0.014182761667009575 0.17848318979719283 chr19 59128983 532654 0.009008340292272573 0.1383812061668459 chr20 63025520 869839 0.013801377600692544 0.12205872869309507 chr21 48129895 438335 0.009107333394348773 0.10068777011105418 chr22 51304566 384895 0.007502158774718024 0.090218724100765 chrMT 16571 430 0.025948946955524712 0.15898301515389648 chrX 155270560 1318302 0.00849035387004465 0.10643906245929761 chrY 59373566 80896 0.0013624918536979907 0.043518827058323696