BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004087.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 = 2,905,862 number of mapped reads = 2,593,471 (89.25%) number of supplementary alignments = 29,475 (1.01%) number of secondary alignments = 0 number of mapped bases = 169,909,673 bp number of sequenced bases = 169,821,813 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 185,826 duplication rate = 5.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.061 >>>>>>> ACTG content number of A's = 47,433,618 bp (27.93%) number of C's = 30,317,418 bp (17.85%) number of T's = 54,775,884 bp (32.25%) number of G's = 37,214,733 bp (21.91%) number of N's = 80,160 bp (0.05%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,444,228 number of insertions = 13,076 mapped reads with insertion percentage = 0.5% number of deletions = 53,005 mapped reads with deletion percentage = 2.02% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.0549X std coverageData = 0.5484X There is a 4.08% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 11995969 0.04812814087231502 1.0215930331306262 chr2 243199373 13722480 0.05642481652286168 0.6127392905462506 chr3 198022430 11753185 0.0593527965493606 0.3090183377110899 chr4 191154276 12099958 0.06329943673350001 0.3453694734189435 chr5 180915260 9176687 0.050723675824803284 0.2917041821677606 chr6 171115067 9316614 0.05444648541674007 0.34006086068196734 chr7 159138663 12988723 0.08161890237823602 0.7402237408584186 chr8 146364022 11279588 0.07706530502420875 0.8852641024668703 chr9 141213431 5672040 0.04016643431034545 0.48666821329208004 chr10 135534747 7849706 0.05791655773703551 0.4936156022684225 chr11 135006516 7191725 0.053269465897483055 0.4439418153153491 chr12 133851895 7537990 0.05631590049584281 0.31406100343914 chr13 115169878 5200830 0.04515790144363963 0.26723013113981436 chr14 107349540 4448158 0.0414362092282836 0.30096299677131283 chr15 102531392 4184739 0.04081422204820939 0.2575142184949213 chr16 90354753 4854261 0.053724467599396794 0.3513269438811149 chr17 81195210 3432001 0.04226851559346912 0.2964373694925523 chr18 78077248 5511596 0.07059157617850466 0.997338213694235 chr19 59128983 2282142 0.03859599614625538 0.7327985355322726 chr20 63025520 4884849 0.07750588967770516 0.3859560577903593 chr21 48129895 2351855 0.048864744043177324 0.31003199444374074 chr22 51304566 988863 0.019274366340025176 0.16753700914046413 chrMT 16571 22505 1.358095467986241 1.670783262441745 chrX 155270560 10681092 0.0687901943549376 0.3939641589544131 chrY 59373566 482117 0.008120061375461262 0.17829197929730853