BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240198.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 = 1,111,658 number of mapped reads = 843,185 (75.85%) number of supplementary alignments = 4,067 (0.37%) number of secondary alignments = 0 number of mapped bases = 52,845,697 bp number of sequenced bases = 52,820,380 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,094 duplication rate = 5.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7445 >>>>>>> ACTG content number of A's = 14,330,031 bp (27.13%) number of C's = 9,277,179 bp (17.56%) number of T's = 17,101,674 bp (32.38%) number of G's = 12,098,517 bp (22.91%) number of N's = 12,979 bp (0.02%) GC percentage = 40.47% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 454,621 number of insertions = 3,849 mapped reads with insertion percentage = 0.45% number of deletions = 14,500 mapped reads with deletion percentage = 1.7% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.2003X There is a 1.38% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 4012726 0.016099161494165345 0.2935905247983261 chr2 243199373 4508095 0.018536622625256523 0.21806444418917115 chr3 198022430 3728565 0.018829003360881898 0.16730645148416295 chr4 191154276 3321522 0.017376132354998953 0.18544488374367454 chr5 180915260 3074619 0.01699480187575111 0.15928972010512357 chr6 171115067 3463479 0.020240643098950486 0.19247556777169925 chr7 159138663 2898606 0.0182143417907187 0.2380829932095344 chr8 146364022 2666749 0.018219976217926016 0.22873745988746227 chr9 141213431 2136884 0.015132299986394353 0.1883869179564879 chr10 135534747 2609546 0.019253704734476688 0.19376245331250097 chr11 135006516 2255786 0.016708719451733724 0.1782189261402961 chr12 133851895 2329710 0.01740513274018272 0.16116279379715132 chr13 115169878 1602368 0.013913082377320918 0.1430684979251545 chr14 107349540 1609498 0.014993059122563544 0.153266050768994 chr15 102531392 1905209 0.018581713978875855 0.2487396726363927 chr16 90354753 1805811 0.019985788683413257 0.18674264336534657 chr17 81195210 1288999 0.015875308407971356 0.15557006088289915 chr18 78077248 1493421 0.019127480005442815 0.2785219433194938 chr19 59128983 891928 0.015084446827032354 0.22008823106486183 chr20 63025520 997839 0.01583230094729881 0.15381219555056538 chr21 48129895 730052 0.015168368848508812 0.15351324370157776 chr22 51304566 498554 0.009717536641865365 0.1176637832774146 chrMT 16571 37987 2.292378251161668 2.4321959553844437 chrX 155270560 2843189 0.018311191767454178 0.16885650929251722 chrY 59373566 134555 0.0022662442070600915 0.07343817792684412