BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716366.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 = 1,278,319 number of mapped reads = 875,278 (68.47%) number of supplementary alignments = 2,475 (0.19%) number of secondary alignments = 0 number of mapped bases = 48,275,249 bp number of sequenced bases = 48,261,451 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,129 duplication rate = 1.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.5494 >>>>>>> ACTG content number of A's = 11,489,814 bp (23.81%) number of C's = 9,664,733 bp (20.03%) number of T's = 14,874,220 bp (30.82%) number of G's = 12,231,390 bp (25.34%) number of N's = 1,294 bp (0%) GC percentage = 45.37% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 260,893 number of insertions = 3,626 mapped reads with insertion percentage = 0.41% number of deletions = 8,115 mapped reads with deletion percentage = 0.92% homopolymer indels = 34.68% >>>>>>> Coverage mean coverageData = 0.0156X std coverageData = 0.1568X There is a 1.43% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% 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 4779318 0.019174748615771755 0.18874762834291306 chr2 243199373 4238163 0.017426702000584517 0.20079332283156381 chr3 198022430 3171174 0.016014216167330134 0.14690415119159697 chr4 191154276 3132484 0.016387203391673016 0.15061014936744507 chr5 180915260 2997763 0.01656998420144326 0.1386135166660386 chr6 171115067 2026126 0.01184072236023494 0.12072597070901792 chr7 159138663 2772282 0.017420543491684357 0.17494689226296317 chr8 146364022 2958760 0.02021507717244884 0.1609185612829693 chr9 141213431 2110642 0.014946467804468259 0.1416764791786012 chr10 135534747 2499700 0.018443240979377783 0.22680450020881246 chr11 135006516 1981457 0.01467675086141768 0.1574299867508366 chr12 133851895 2354359 0.017589284036658576 0.1432072319047486 chr13 115169878 831832 0.007222652436950572 0.09328915797298135 chr14 107349540 1598931 0.014894623675145697 0.1342597035583693 chr15 102531392 973321 0.009492907303940631 0.1075016232598572 chr16 90354753 1343579 0.014870042309783083 0.14019293015484205 chr17 81195210 1883002 0.023191047846295366 0.17272543456589853 chr18 78077248 1289610 0.016517103676604996 0.1710395547379741 chr19 59128983 1250541 0.02114937441085364 0.18530294944373257 chr20 63025520 1206707 0.01914632358447816 0.15384329051792384 chr21 48129895 635861 0.013211352320631491 0.13210752580438612 chr22 51304566 513513 0.01000910913075456 0.10963120676060675 chrMT 16571 3107 0.1874962283507332 0.44370826817544834 chrX 155270560 1572516 0.010127586324155719 0.11982113780458638 chrY 59373566 150501 0.002534814903992797 0.08565156856661772