BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008828.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 = 2,766,238 number of mapped reads = 2,227,231 (80.51%) number of supplementary alignments = 20,999 (0.76%) number of secondary alignments = 0 number of mapped bases = 145,177,756 bp number of sequenced bases = 145,087,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 138,814 duplication rate = 4.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3503 >>>>>>> ACTG content number of A's = 40,258,526 bp (27.75%) number of C's = 27,409,202 bp (18.89%) number of T's = 45,166,692 bp (31.13%) number of G's = 32,046,170 bp (22.09%) number of N's = 207,213 bp (0.14%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,354,601 number of insertions = 10,340 mapped reads with insertion percentage = 0.46% number of deletions = 50,937 mapped reads with deletion percentage = 2.26% homopolymer indels = 44.29% >>>>>>> Coverage mean coverageData = 0.0469X std coverageData = 0.6516X There is a 3.62% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 14472392 0.05806361461382277 1.5374869020743493 chr2 243199373 11855187 0.048746782747667694 0.5370017257455718 chr3 198022430 8044616 0.04062477164834307 0.3301021960270397 chr4 191154276 8988497 0.04702221257137873 0.2819830303743936 chr5 180915260 10826064 0.05984052423217367 0.3011196433025318 chr6 171115067 5811685 0.033963607658231525 0.25400574162135797 chr7 159138663 8980122 0.05642954283208977 0.6625362954686116 chr8 146364022 7445072 0.050866817529788846 0.7272433495156139 chr9 141213431 4442489 0.03145939425549401 0.40024060833850517 chr10 135534747 7027419 0.051849574780996936 1.2533856005058983 chr11 135006516 5306212 0.03930337703107604 0.3669133969083729 chr12 133851895 7963615 0.0594957209981973 0.30400786348743575 chr13 115169878 3387923 0.029416745583424164 0.2075893208934304 chr14 107349540 3919498 0.03651154909466776 0.24920726853336592 chr15 102531392 4157869 0.04055215596799856 0.24866199514450987 chr16 90354753 5565772 0.06159910591532468 0.44032267829963656 chr17 81195210 4658243 0.05737090894893923 0.334359267549863 chr18 78077248 2648487 0.03392136720802454 0.6414401109669321 chr19 59128983 3362467 0.05686664693691755 1.0053367812636798 chr20 63025520 3576235 0.05674264964414415 0.29827752326793194 chr21 48129895 1124332 0.023360366774122402 0.2092032446581992 chr22 51304566 1757008 0.034246620466490255 0.22734395526560675 chrMT 16571 209671 12.652887574678655 8.262587726725375 chrX 155270560 9070580 0.058417899697147994 0.36235325693909437 chrY 59373566 576301 0.009706356529099161 0.32100334315887746