BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013247.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,219,870 number of mapped reads = 926,906 (75.98%) number of supplementary alignments = 13,237 (1.09%) number of secondary alignments = 0 number of mapped bases = 58,739,051 bp number of sequenced bases = 58,690,630 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,780 duplication rate = 7.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.578 >>>>>>> ACTG content number of A's = 16,350,447 bp (27.86%) number of C's = 10,346,836 bp (17.63%) number of T's = 19,210,973 bp (32.73%) number of G's = 12,770,164 bp (21.76%) number of N's = 12,210 bp (0.02%) GC percentage = 39.39% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 583,065 number of insertions = 4,533 mapped reads with insertion percentage = 0.49% number of deletions = 27,379 mapped reads with deletion percentage = 2.91% homopolymer indels = 42.25% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.246X There is a 1.29% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 3621982 0.014531486362876505 0.2685444884330054 chr2 243199373 3419410 0.014060110261879664 0.26431172668796044 chr3 198022430 3975472 0.020075867163128945 0.19573421503458638 chr4 191154276 7006435 0.03665329987177478 0.27393985941829385 chr5 180915260 2094714 0.011578426275373343 0.14977010206437685 chr6 171115067 4056920 0.02370872460927126 0.2455070565714212 chr7 159138663 3494089 0.02195625459037569 0.27897762020222316 chr8 146364022 2356143 0.016097829014291503 0.46280175894849024 chr9 141213431 1518503 0.01075324768505908 0.20959693055305215 chr10 135534747 3093393 0.02282361585107028 0.2545407186760708 chr11 135006516 2115326 0.015668325223650685 0.1878455572232192 chr12 133851895 3129104 0.023377360477414233 0.21261846086030717 chr13 115169878 1550562 0.013463259898564797 0.16415324951292296 chr14 107349540 1799633 0.016764235785267454 0.18338234712651394 chr15 102531392 2674571 0.02608538661018081 0.22089450605802 chr16 90354753 2572625 0.02847249219971859 0.24341944463558038 chr17 81195210 1480111 0.018229043314254623 0.20122150687500923 chr18 78077248 2168117 0.02776887064462108 0.36456517452544857 chr19 59128983 843527 0.014265880405891641 0.2441121139728316 chr20 63025520 2015528 0.031979553679208045 0.2506869250421535 chr21 48129895 1058953 0.022001980266111113 0.21516136811341588 chr22 51304566 374825 0.007305879948385101 0.11512532383830072 chrMT 16571 11792 0.7116046104640638 1.1545712944874074 chrX 155270560 2090950 0.013466493583844871 0.16890769422345864 chrY 59373566 216366 0.0036441469592714036 0.11950362137139008