BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068100.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 = 1,994,990 number of mapped reads = 1,163,862 (58.34%) number of supplementary alignments = 9,458 (0.47%) number of secondary alignments = 0 number of mapped bases = 76,216,100 bp number of sequenced bases = 76,182,318 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,423 duplication rate = 3.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8485 >>>>>>> ACTG content number of A's = 20,997,444 bp (27.56%) number of C's = 14,108,908 bp (18.52%) number of T's = 24,004,279 bp (31.51%) number of G's = 17,070,288 bp (22.41%) number of N's = 1,399 bp (0%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 582,510 number of insertions = 6,197 mapped reads with insertion percentage = 0.52% number of deletions = 20,254 mapped reads with deletion percentage = 1.7% homopolymer indels = 46.88% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.3023X There is a 1.97% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.07% 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 10246426 0.041108928671435487 0.6042720142819421 chr2 243199373 4125810 0.01696472301349231 0.4155157673297461 chr3 198022430 6682175 0.03374453590939168 0.22520295925244407 chr4 191154276 1939397 0.010145716018405991 0.12372831593305718 chr5 180915260 2118802 0.011711571483798547 0.2712921406072087 chr6 171115067 1501724 0.00877610619759159 0.14935094543592106 chr7 159138663 4464162 0.028052026552466386 0.218763163856062 chr8 146364022 2717682 0.01856796474204569 0.2585074098703197 chr9 141213431 2741298 0.019412445265209938 0.28570249663773245 chr10 135534747 5223474 0.03853974066148513 0.3289496101641872 chr11 135006516 6207544 0.04597958812595386 0.28315672873898184 chr12 133851895 4401224 0.03288129764617826 0.22816773972128201 chr13 115169878 535172 0.004646805304421699 0.08015752475786656 chr14 107349540 669582 0.0062373998062776985 0.15814400636096404 chr15 102531392 2201039 0.02146697666993539 0.17682766375398012 chr16 90354753 606189 0.0067089885133104175 0.12645466556520474 chr17 81195210 3552694 0.04375497027472433 0.29561475320431374 chr18 78077248 6624892 0.08485048038578409 0.4689462993866936 chr19 59128983 2615593 0.04423537945849669 0.39627661249109586 chr20 63025520 346408 0.005496313239462364 0.09943875977961081 chr21 48129895 1188219 0.02468775383781743 0.19976604039347481 chr22 51304566 456013 0.008888351184960808 0.111852646390832 chrMT 16571 17932 1.0821314344336492 1.2239901806864912 chrX 155270560 4847346 0.03121870623767957 0.28160737152905085 chrY 59373566 185303 0.003120968007884182 0.07512137947567836