BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008789.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 = 1,437,033 number of mapped reads = 1,119,346 (77.89%) number of supplementary alignments = 5,477 (0.38%) number of secondary alignments = 0 number of mapped bases = 75,586,076 bp number of sequenced bases = 75,549,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,889 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0557 >>>>>>> ACTG content number of A's = 22,494,032 bp (29.77%) number of C's = 13,205,576 bp (17.48%) number of T's = 23,358,707 bp (30.92%) number of G's = 16,477,496 bp (21.81%) number of N's = 13,937 bp (0.02%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 668,951 number of insertions = 6,322 mapped reads with insertion percentage = 0.56% number of deletions = 22,326 mapped reads with deletion percentage = 1.97% homopolymer indels = 47.56% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2157X There is a 2.26% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6079966 0.02439298235489652 0.33184351202065554 chr2 243199373 6918537 0.028448005085934164 0.24155009148593287 chr3 198022430 6354527 0.032089935468421434 0.18903419321817794 chr4 191154276 4676317 0.024463575170037003 0.16637590450700215 chr5 180915260 3498271 0.019336516996963107 0.14620275757467863 chr6 171115067 3472229 0.020291778280401223 0.16089388431760232 chr7 159138663 4604528 0.028934062365473058 0.30311954755259174 chr8 146364022 7247309 0.049515645313436385 0.30909772133292857 chr9 141213431 1906147 0.013498340678373575 0.1723796304329097 chr10 135534747 4418666 0.032601720944666686 0.2399407615849164 chr11 135006516 2795916 0.020709489310871486 0.19603025591792445 chr12 133851895 2912446 0.021758720711425115 0.15560996406089994 chr13 115169878 2972897 0.025813147080002985 0.16855450101245492 chr14 107349540 3160879 0.029444737257374367 0.18336592572018812 chr15 102531392 1763420 0.017198830188514362 0.13938161850195604 chr16 90354753 1686548 0.01866584705289383 0.1578099767733509 chr17 81195210 1495057 0.018413118212268927 0.15671981312118782 chr18 78077248 999952 0.012807213696876202 0.3047654950055557 chr19 59128983 1080081 0.01826652421875749 0.21746965965340934 chr20 63025520 1409836 0.022369287869421783 0.15958282464030246 chr21 48129895 488990 0.010159797772257763 0.10996944378468623 chr22 51304566 792569 0.015448313118953194 0.1297197592079562 chrMT 16571 24968 1.5067286222919558 1.3965237634857524 chrX 155270560 4651610 0.02995809379447076 0.1933804467108653 chrY 59373566 174410 0.0029375025242714915 0.07624534226685166