BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716304.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 = 748,142 number of mapped reads = 682,757 (91.26%) number of supplementary alignments = 2,255 (0.3%) number of secondary alignments = 0 number of mapped bases = 39,387,231 bp number of sequenced bases = 39,374,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,425 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4828 >>>>>>> ACTG content number of A's = 9,703,023 bp (24.64%) number of C's = 6,936,903 bp (17.62%) number of T's = 12,467,366 bp (31.66%) number of G's = 10,267,208 bp (26.08%) number of N's = 418 bp (0%) GC percentage = 43.69% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 194,257 number of insertions = 2,206 mapped reads with insertion percentage = 0.32% number of deletions = 7,517 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 0.1404X There is a 1.19% 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 3173793 0.012733340391557138 0.18343541334592844 chr2 243199373 3336619 0.013719685864486172 0.16643542604519013 chr3 198022430 2618279 0.01322213347245562 0.12120989673761688 chr4 191154276 2581936 0.01350707948589128 0.12870505994289486 chr5 180915260 2381015 0.013160940652546391 0.1204313946591817 chr6 171115067 2365624 0.013824755712482057 0.1336210576347005 chr7 159138663 2203646 0.013847332624630634 0.18134331867660017 chr8 146364022 1995258 0.013632161597745654 0.14435423579543288 chr9 141213431 1566318 0.011091848621679619 0.12303135025332927 chr10 135534747 1864674 0.013757903720438568 0.16174210401572225 chr11 135006516 1794941 0.01329521754342583 0.1338658951315676 chr12 133851895 1722879 0.012871532375391473 0.119301543677106 chr13 115169878 1064497 0.009242842125785702 0.10079731168025081 chr14 107349540 1212905 0.011298651116716477 0.11341582028015024 chr15 102531392 1150644 0.011222358124231845 0.11157285621073772 chr16 90354753 1222618 0.013531308087356511 0.12984104361830187 chr17 81195210 1068024 0.01315378086958578 0.12580176433070248 chr18 78077248 1044112 0.01337280740222811 0.18083178478269518 chr19 59128983 826353 0.013975430627650064 0.16125954254670252 chr20 63025520 790417 0.012541221397300649 0.1203985340254175 chr21 48129895 546846 0.01136187810091836 0.11521151717060292 chr22 51304566 456865 0.008904957894001092 0.10018724598598325 chrMT 16571 1093 0.0659586023776477 0.27715583160694623 chrX 155270560 2273283 0.014640785735557339 0.13282499609524479 chrY 59373566 124592 0.002098442259641269 0.06749278149916035