BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234075.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 = 3,751,625 number of mapped reads = 3,514,070 (93.67%) number of supplementary alignments = 35,417 (0.94%) number of secondary alignments = 0 number of mapped bases = 226,556,225 bp number of sequenced bases = 226,470,737 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 540,972 duplication rate = 12.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6916 >>>>>>> ACTG content number of A's = 58,915,169 bp (26.01%) number of C's = 40,573,082 bp (17.92%) number of T's = 73,890,854 bp (32.63%) number of G's = 53,070,137 bp (23.43%) number of N's = 21,495 bp (0.01%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,260,076 number of insertions = 15,728 mapped reads with insertion percentage = 0.44% number of deletions = 49,710 mapped reads with deletion percentage = 1.4% homopolymer indels = 43.9% >>>>>>> Coverage mean coverageData = 0.0732X std coverageData = 0.8479X There is a 5.05% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% 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 0.01% 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 15955112 0.06401232597129618 1.1619120611448652 chr2 243199373 11820288 0.04860328320007634 1.7010794520854802 chr3 198022430 28949010 0.14619056033197855 0.5289835052578912 chr4 191154276 3006570 0.015728499842713434 0.2970648750155164 chr5 180915260 11420971 0.06312884275212605 0.3542519454799215 chr6 171115067 17284464 0.1010107660478548 0.6635499654351676 chr7 159138663 19054854 0.11973742672451634 1.3001397622206436 chr8 146364022 13185407 0.0900863943189536 1.15197391154563 chr9 141213431 9997484 0.07079697681164619 0.5342490698229269 chr10 135534747 8309050 0.06130568126563146 0.681341782016927 chr11 135006516 9399612 0.06962339506635369 0.5485010511344752 chr12 133851895 10889941 0.08135813841111476 0.40086584612316156 chr13 115169878 12121383 0.10524785829850405 0.5012249817935023 chr14 107349540 10225548 0.09525469787760618 0.45973030488163963 chr15 102531392 4797642 0.04679193275753049 0.33782690456206 chr16 90354753 5883880 0.0651197618790458 0.4374083377053126 chr17 81195210 3580962 0.04410311889088039 0.35006486093341604 chr18 78077248 3994173 0.05115668267406146 1.4771884315764239 chr19 59128983 5621036 0.09506397226551318 0.6918500483269765 chr20 63025520 5602309 0.08888953236720618 0.4750123235013124 chr21 48129895 4299709 0.08933551589921399 0.44029457972774927 chr22 51304566 1778606 0.03466759664237292 0.24337191094264932 chrMT 16571 631257 38.094080019310844 26.1022962695506 chrX 155270560 8148968 0.05248237656900316 0.4209838138558582 chrY 59373566 597989 0.010071636930144973 0.287158695883018