BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716402.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 = 1,695,394 number of mapped reads = 1,551,216 (91.5%) number of supplementary alignments = 6,822 (0.4%) number of secondary alignments = 0 number of mapped bases = 89,011,356 bp number of sequenced bases = 88,988,764 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,484 duplication rate = 2.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.971 >>>>>>> ACTG content number of A's = 23,296,014 bp (26.18%) number of C's = 18,658,710 bp (20.97%) number of T's = 26,523,124 bp (29.81%) number of G's = 20,509,018 bp (23.05%) number of N's = 1,898 bp (0%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 428,757 number of insertions = 6,176 mapped reads with insertion percentage = 0.4% number of deletions = 13,247 mapped reads with deletion percentage = 0.85% homopolymer indels = 40.19% >>>>>>> Coverage mean coverageData = 0.0288X std coverageData = 0.2358X There is a 2.58% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 7056619 0.02831133969371334 0.3861084530131229 chr2 243199373 7497402 0.030828212702670086 0.25435743472081684 chr3 198022430 6006331 0.030331569004581956 0.18967384796776354 chr4 191154276 5644241 0.029527150101523233 0.19985051899540326 chr5 180915260 5537681 0.030609253194009173 0.1920958626955305 chr6 171115067 5144941 0.030067141895809793 0.20135666112480002 chr7 159138663 4787466 0.03008361330772271 0.2397018830963135 chr8 146364022 4554267 0.031116027953918893 0.21585327031536788 chr9 141213431 3608802 0.025555656954471987 0.23003832787789796 chr10 135534747 4309375 0.03179535208045211 0.22813097562803003 chr11 135006516 4032935 0.02987215076344908 0.23879464025651528 chr12 133851895 3970737 0.02966515341452581 0.18946969849411596 chr13 115169878 2809806 0.024397056320577155 0.16946521869519257 chr14 107349540 2698480 0.025137322432867433 0.17968748631661066 chr15 102531392 2587398 0.02523517870507405 0.1745527072075544 chr16 90354753 2608151 0.028865675721563868 0.1971225402485563 chr17 81195210 2342092 0.02884519911950471 0.19270892157602584 chr18 78077248 2354479 0.030155763174439756 0.4035789509036889 chr19 59128983 1888206 0.03193367963051216 0.28233596641059333 chr20 63025520 1904633 0.030220028331380686 0.19740124978362975 chr21 48129895 1195210 0.024833006596004417 0.18760877122819256 chr22 51304566 1044839 0.02036541932739476 0.15589323664659854 chrMT 16571 47353 2.8575825236859576 2.1969566393997733 chrX 155270560 5124714 0.03300505904016834 0.22216150708111973 chrY 59373566 255198 0.004298175386669549 0.10582027064280472