BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525054.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,218,319 number of mapped reads = 953,608 (78.27%) number of supplementary alignments = 2,724 (0.22%) number of secondary alignments = 0 number of mapped bases = 54,978,510 bp number of sequenced bases = 54,960,681 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,411 duplication rate = 4.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0738 >>>>>>> ACTG content number of A's = 13,649,255 bp (24.83%) number of C's = 10,880,645 bp (19.8%) number of T's = 18,082,269 bp (32.9%) number of G's = 12,343,128 bp (22.46%) number of N's = 5,384 bp (0.01%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 272,217 number of insertions = 4,520 mapped reads with insertion percentage = 0.47% number of deletions = 11,151 mapped reads with deletion percentage = 1.16% homopolymer indels = 43.06% >>>>>>> Coverage mean coverageData = 0.0178X std coverageData = 0.1929X There is a 1.6% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4445472 0.01783534974622992 0.33835498672119113 chr2 243199373 4687476 0.01927421087553544 0.22856948958896384 chr3 198022430 3608540 0.018222885154979666 0.1466719765032457 chr4 191154276 3382898 0.017697213323127545 0.15809009518356118 chr5 180915260 3349796 0.01851582890243753 0.14806552854056498 chr6 171115067 3093545 0.018078741131545124 0.15712936974072153 chr7 159138663 3051603 0.01917574863626949 0.21901250290169744 chr8 146364022 2778436 0.018983053089371923 0.2097605612347821 chr9 141213431 2236845 0.015840171746836176 0.1566008773261742 chr10 135534747 2646878 0.019529147016447375 0.21145624830164417 chr11 135006516 2867533 0.0212399600031157 0.17727016348648833 chr12 133851895 2440292 0.01823128465981001 0.15077842389379476 chr13 115169878 1778749 0.015444567893004106 0.13493724380291297 chr14 107349540 1643330 0.015308216504700439 0.13678728185715397 chr15 102531392 1583120 0.015440344358145454 0.13510184595505365 chr16 90354753 1695535 0.018765310553170347 0.16113994679482047 chr17 81195210 1436694 0.017694319652600196 0.14886059260408543 chr18 78077248 1470139 0.018829288142942744 0.2291023826213591 chr19 59128983 1059080 0.017911351527896226 0.2398662242503659 chr20 63025520 1138836 0.018069442346528835 0.1484660883848946 chr21 48129895 735466 0.015280856108246237 0.15106688906517768 chr22 51304566 611001 0.011909290880659628 0.11881534919214513 chrMT 16571 31824 1.9204634602619033 1.6556954102587664 chrX 155270560 3020172 0.019451027934722462 0.1618746435800071 chrY 59373566 185250 0.003120075354746252 0.11920156123183585