BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716541.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 = 1,365,078 number of mapped reads = 1,204,187 (88.21%) number of supplementary alignments = 5,042 (0.37%) number of secondary alignments = 0 number of mapped bases = 69,466,444 bp number of sequenced bases = 69,444,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,705 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1363 >>>>>>> ACTG content number of A's = 17,288,994 bp (24.9%) number of C's = 12,898,976 bp (18.57%) number of T's = 22,447,449 bp (32.32%) number of G's = 16,807,359 bp (24.2%) number of N's = 2,110 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 351,269 number of insertions = 4,471 mapped reads with insertion percentage = 0.37% number of deletions = 13,517 mapped reads with deletion percentage = 1.11% homopolymer indels = 41.7% >>>>>>> Coverage mean coverageData = 0.0224X std coverageData = 0.2238X There is a 2.05% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5635165 0.022608429128046184 0.40221829701071593 chr2 243199373 5888810 0.02421391933440552 0.290444089931458 chr3 198022430 4637461 0.023418867246503338 0.1654826290558847 chr4 191154276 4415035 0.023096710638060746 0.17260963580763192 chr5 180915260 4196280 0.023194726636105764 0.16444469866757203 chr6 171115067 4087744 0.023888860704475545 0.19183367422088984 chr7 159138663 3818015 0.023991749886701007 0.25897509175690026 chr8 146364022 3442187 0.02351798586130682 0.21235504399213495 chr9 141213431 2883688 0.020420777114324204 0.18820685261833214 chr10 135534747 3339501 0.024639445410998554 0.21503114314713515 chr11 135006516 3149668 0.02332974802490274 0.19631639011556207 chr12 133851895 3206123 0.023952765106538088 0.16858358696871015 chr13 115169878 2220152 0.019277193295281603 0.15096001405982176 chr14 107349540 2119265 0.019741724091225727 0.15687327765102513 chr15 102531392 1991976 0.01942796212110336 0.1510043682946984 chr16 90354753 1998549 0.022118913877170358 0.16848499385529897 chr17 81195210 1858055 0.022883800657698895 0.17067817834842042 chr18 78077248 1830007 0.023438415759735792 0.30092848951495654 chr19 59128983 1448248 0.024493030769698845 0.28499809069176274 chr20 63025520 1437953 0.02281540874236341 0.16409308334050457 chr21 48129895 912439 0.018957843145097242 0.15862743524150352 chr22 51304566 818996 0.01596341347084 0.13617256543365497 chrMT 16571 4475 0.270050087502263 0.5337290382627854 chrX 155270560 3912156 0.025195735753126672 0.18614244529894766 chrY 59373566 214496 0.003612651461763304 0.10366319116383285