BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174058.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,787,274 number of mapped reads = 6,595,543 (97.18%) number of supplementary alignments = 667,088 (9.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,302,333 number of mapped paired reads (second in pair) = 3,293,210 number of mapped paired reads (both in pair) = 6,464,108 number of mapped paired reads (singletons) = 131,435 number of mapped bases = 778,190,777 bp number of sequenced bases = 777,748,344 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,246,633 duplication rate = 65.58% >>>>>>> Insert size mean insert size = 951,464.983 std insert size = 8,636,345.8645 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.605 >>>>>>> ACTG content number of A's = 234,402,607 bp (30.14%) number of C's = 151,897,332 bp (19.53%) number of T's = 234,002,190 bp (30.09%) number of G's = 157,436,731 bp (20.24%) number of N's = 9,484 bp (0%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 7,874,112 number of insertions = 82,499 mapped reads with insertion percentage = 1.21% number of deletions = 180,241 mapped reads with deletion percentage = 2.67% homopolymer indels = 42.46% >>>>>>> Coverage mean coverageData = 0.2514X std coverageData = 3.6965X There is a 4.85% of reference with a coverageData >= 1X There is a 3.88% of reference with a coverageData >= 2X There is a 3.07% of reference with a coverageData >= 3X There is a 2.57% of reference with a coverageData >= 4X There is a 2.02% of reference with a coverageData >= 5X There is a 1.66% of reference with a coverageData >= 6X There is a 1.27% of reference with a coverageData >= 7X There is a 1.04% of reference with a coverageData >= 8X There is a 0.79% of reference with a coverageData >= 9X There is a 0.66% of reference with a coverageData >= 10X There is a 0.5% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 71085817 0.28519815402987503 2.0433774730393846 chr2 243199373 57264104 0.23546156099670537 10.865966467856397 chr3 198022430 48767164 0.2462709098156204 1.4970421688582523 chr4 191154276 48606063 0.2542766189546291 1.9857123181088399 chr5 180915260 39870394 0.22038159743959687 1.4026695387182309 chr6 171115067 38135470 0.22286447750390093 1.4814217229514746 chr7 159138663 68729338 0.43188334440135395 4.030623324155817 chr8 146364022 77690274 0.530801715738585 2.904741075798556 chr9 141213431 26989507 0.1911256373340295 1.7061500634075155 chr10 135534747 35284235 0.2603334995711469 4.7662608783592315 chr11 135006516 32576237 0.24129381281122758 1.5187801656958035 chr12 133851895 29665210 0.22162712003442311 1.4084956426501156 chr13 115169878 20132983 0.1748111863068918 1.2574235463080279 chr14 107349540 26106495 0.24319149388064448 1.4852386584060724 chr15 102531392 18658060 0.18197412164266724 1.2717917670050214 chr16 90354753 17814084 0.1971571323978939 1.897035309916912 chr17 81195210 19267577 0.23729942936288975 1.5517782733569523 chr18 78077248 14379085 0.18416485427355225 2.230422692956126 chr19 59128983 10126216 0.1712563870750153 1.5122662284726238 chr20 63025520 26030991 0.4130230262281057 1.9598170718109162 chr21 48129895 9574950 0.1989397649839045 1.459771748680258 chr22 51304566 8029242 0.15650150904697255 1.1402666731352458 chrMT 16571 1846749 111.4446321887635 83.00278829161923 chrX 155270560 30021383 0.19334884217587675 1.3147405374222396 chrY 59373566 1539149 0.02592313555833921 1.1280325781645095