BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236113.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 = 3,979,741 number of mapped reads = 3,284,423 (82.53%) number of supplementary alignments = 19,945 (0.5%) number of secondary alignments = 0 number of mapped bases = 213,401,114 bp number of sequenced bases = 213,284,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 259,523 duplication rate = 6.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9181 >>>>>>> ACTG content number of A's = 57,236,701 bp (26.84%) number of C's = 38,387,912 bp (18%) number of T's = 68,151,985 bp (31.95%) number of G's = 49,388,319 bp (23.16%) number of N's = 119,130 bp (0.06%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,803,175 number of insertions = 14,960 mapped reads with insertion percentage = 0.45% number of deletions = 67,471 mapped reads with deletion percentage = 2.03% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 0.0689X std coverageData = 0.6188X There is a 5.07% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% 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 13944503 0.05594571016133998 1.207101595727938 chr2 243199373 18783560 0.07723523201681938 0.6784541950115617 chr3 198022430 12179880 0.06150757770218253 0.31592203607346997 chr4 191154276 11083850 0.05798379315354683 0.3512161422720808 chr5 180915260 12745332 0.07044918156710496 0.3433216249554835 chr6 171115067 25789680 0.1507154247264503 0.9781200665246708 chr7 159138663 10063711 0.06323862982309962 0.7198371174386554 chr8 146364022 13738180 0.09386309430605835 0.6313607644052264 chr9 141213431 8655047 0.061290536875348633 0.5149047173042346 chr10 135534747 10425807 0.07692349918209535 0.472184991768542 chr11 135006516 5083039 0.037650323485127195 0.4140006286160426 chr12 133851895 6387863 0.0477233661876808 0.2936689191957313 chr13 115169878 5138392 0.04461576315987762 0.27122362012601914 chr14 107349540 10295442 0.09590578590276214 0.4287439196343398 chr15 102531392 3755944 0.03663213701419366 0.26420508681315746 chr16 90354753 2011965 0.02226739527471233 0.2932010437445168 chr17 81195210 6469360 0.07967662131793242 0.4439515396043648 chr18 78077248 3905949 0.05002672481489102 1.015308235430459 chr19 59128983 4980319 0.0842280510726863 0.7338334740873412 chr20 63025520 4619185 0.07329070827182385 0.3554285991702741 chr21 48129895 3050494 0.06338044161534115 0.36276923524560944 chr22 51304566 2952334 0.05754524850673135 0.3049885725407243 chrMT 16571 271801 16.402208677810634 9.53516998311139 chrX 155270560 16454291 0.1059717373338513 0.4879572953069622 chrY 59373566 615186 0.010361277609635237 0.22453032445217633