BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717073.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 = 537,985 number of mapped reads = 486,254 (90.38%) number of supplementary alignments = 2,891 (0.54%) number of secondary alignments = 0 number of mapped bases = 28,695,376 bp number of sequenced bases = 28,687,343 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,585 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3837 >>>>>>> ACTG content number of A's = 7,141,882 bp (24.9%) number of C's = 5,832,312 bp (20.33%) number of T's = 8,708,628 bp (30.36%) number of G's = 7,004,326 bp (24.42%) number of N's = 195 bp (0%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 139,672 number of insertions = 1,762 mapped reads with insertion percentage = 0.36% number of deletions = 5,006 mapped reads with deletion percentage = 1.02% homopolymer indels = 43.42% >>>>>>> Coverage mean coverageData = 0.0093X std coverageData = 0.1167X There is a 0.86% of reference with a coverageData >= 1X There is a 0.05% 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 2327964 0.009339852356877378 0.14611453228412127 chr2 243199373 2425492 0.009973265843904951 0.14002635151187431 chr3 198022430 1872081 0.00945388358278403 0.10329084671111777 chr4 191154276 1804609 0.00944058923379773 0.11142953250859379 chr5 180915260 1727702 0.009549785905290688 0.10332107820582351 chr6 171115067 1620752 0.009471708297902254 0.10614128067289602 chr7 159138663 1587635 0.009976425402040735 0.1339818315625951 chr8 146364022 1452569 0.009924358323522977 0.1333882949799112 chr9 141213431 1185397 0.008394364414246121 0.1037694231099006 chr10 135534747 1414243 0.010434541925990389 0.12956243742836743 chr11 135006516 1286677 0.009530480736203873 0.11297624089853131 chr12 133851895 1326086 0.009907114127894865 0.10639215375811523 chr13 115169878 873322 0.007582902883686305 0.0929115511594211 chr14 107349540 880388 0.008201134350459256 0.09664991697259724 chr15 102531392 837296 0.008166240442731919 0.0962385965271098 chr16 90354753 895448 0.009910358561878864 0.10714341866789298 chr17 81195210 824170 0.01015047562534785 0.1093335828000528 chr18 78077248 756174 0.009684946887472264 0.1433344639120784 chr19 59128983 642126 0.010859750454358398 0.13195238046238203 chr20 63025520 658116 0.010442055852930687 0.10998875670943746 chr21 48129895 244585 0.005081768825799433 0.08560509014168241 chr22 51304566 371030 0.0072319099239627135 0.09114243234546222 chrMT 16571 1222 0.07374328646430511 0.3064181502320991 chrX 155270560 1580884 0.01018147934804898 0.10926134789090991 chrY 59373566 99408 0.0016742804365161425 0.06561593031027624