BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716575.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 = 1,414,920 number of mapped reads = 1,294,848 (91.51%) number of supplementary alignments = 8,731 (0.62%) number of secondary alignments = 0 number of mapped bases = 75,234,713 bp number of sequenced bases = 75,214,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,115 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2659 >>>>>>> ACTG content number of A's = 19,043,010 bp (25.32%) number of C's = 15,767,819 bp (20.96%) number of T's = 22,427,812 bp (29.82%) number of G's = 17,974,584 bp (23.9%) number of N's = 876 bp (0%) GC percentage = 44.86% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 366,337 number of insertions = 4,731 mapped reads with insertion percentage = 0.36% number of deletions = 13,125 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.0243X std coverageData = 0.2437X There is a 2.18% of reference with a coverageData >= 1X There is a 0.18% 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 6878288 0.027595871065051427 0.3469083184159205 chr2 243199373 7336921 0.030168338468537087 0.2954588384930662 chr3 198022430 5618666 0.028373886735962184 0.19248985855338907 chr4 191154276 4188980 0.021914131808382878 0.1832694939031328 chr5 180915260 3802433 0.02101775715326612 0.15781070430281097 chr6 171115067 4138793 0.024187192119090248 0.17993687877817408 chr7 159138663 4089971 0.02570067463743867 0.4825701249691427 chr8 146364022 5116596 0.034958017209994405 0.24954777549675825 chr9 141213431 3216499 0.022777571348719654 0.18358106940353758 chr10 135534747 3637366 0.026837147524981175 0.3268048588703779 chr11 135006516 2292537 0.016980935942380735 0.17055096205640716 chr12 133851895 3460072 0.025850003841932905 0.18852889354176827 chr13 115169878 1894720 0.01645152389585756 0.13814055578682838 chr14 107349540 2425786 0.02259707866470597 0.16733796542531165 chr15 102531392 1806655 0.017620505922712918 0.14490638818892485 chr16 90354753 2323405 0.025714253239118478 0.1810962883660131 chr17 81195210 3273707 0.04031896709177795 0.2272029670343069 chr18 78077248 1711756 0.0219238772350173 0.24835683512858145 chr19 59128983 1623836 0.02746260662051299 0.31785768414980126 chr20 63025520 1780697 0.02825358680102917 0.18707132678165084 chr21 48129895 583040 0.012113884727984551 0.13405068584065222 chr22 51304566 1206109 0.023508804265101862 0.16729837128074293 chrMT 16571 75581 4.5610403717337515 3.4104800021534682 chrX 155270560 2569569 0.016548977475189117 0.15548660444328077 chrY 59373566 182730 0.003077632224414481 0.09575269521059478