BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524599.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 = 1,232,319 number of mapped reads = 1,148,676 (93.21%) number of supplementary alignments = 2,468 (0.2%) number of secondary alignments = 0 number of mapped bases = 66,941,839 bp number of sequenced bases = 66,920,621 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,385 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4372 >>>>>>> ACTG content number of A's = 16,024,405 bp (23.95%) number of C's = 12,392,637 bp (18.52%) number of T's = 21,501,137 bp (32.13%) number of G's = 17,002,092 bp (25.41%) number of N's = 350 bp (0%) GC percentage = 43.92% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 314,237 number of insertions = 4,340 mapped reads with insertion percentage = 0.38% number of deletions = 12,595 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.0216X std coverageData = 0.2029X There is a 1.96% of reference with a coverageData >= 1X There is a 0.15% 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 7052682 0.028295544346908567 0.3347924709667936 chr2 243199373 5952235 0.024474713592292033 0.23162848325237537 chr3 198022430 4154071 0.02097778014339083 0.1566754571338865 chr4 191154276 3002082 0.015705021424684218 0.1508079128339785 chr5 180915260 4055500 0.02241657226703817 0.16144314097745854 chr6 171115067 4210371 0.02460549543541949 0.17848408450497452 chr7 159138663 3971452 0.024955921616609283 0.25131217341462114 chr8 146364022 5649842 0.038601303262901586 0.2638299603510551 chr9 141213431 2505639 0.01774363091567402 0.1854427222778132 chr10 135534747 2698732 0.019911735254133762 0.19789235587287635 chr11 135006516 3428357 0.025394011352755742 0.2050842060499407 chr12 133851895 2278133 0.017019803866056584 0.14360642965903256 chr13 115169878 1959386 0.017013007515732544 0.1426783092267959 chr14 107349540 1212822 0.01129787794153566 0.1194883242308967 chr15 102531392 1773889 0.017300935502758023 0.1458387765845347 chr16 90354753 1890107 0.020918733516984988 0.1611891142667688 chr17 81195210 1648376 0.020301394626604206 0.15593603277384693 chr18 78077248 1629057 0.020864682628158205 0.2670160953636496 chr19 59128983 1468339 0.024832813376817253 0.2488435606825675 chr20 63025520 1310578 0.0207944020136605 0.15779158993248119 chr21 48129895 600367 0.012473889668780703 0.12983163028393002 chr22 51304566 1426319 0.0278010148258539 0.18086375806590355 chrMT 16571 5628 0.3396294731760304 0.6306325859374698 chrX 155270560 2903273 0.01869815501406062 0.16296270336046823 chrY 59373566 154602 0.002603886045854143 0.07765417409411567