BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008697.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 = 1,671,523 number of mapped reads = 1,180,623 (70.63%) number of supplementary alignments = 5,543 (0.33%) number of secondary alignments = 0 number of mapped bases = 70,247,481 bp number of sequenced bases = 70,202,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,308 duplication rate = 4.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8707 >>>>>>> ACTG content number of A's = 19,781,743 bp (28.18%) number of C's = 12,054,890 bp (17.17%) number of T's = 22,010,389 bp (31.35%) number of G's = 16,328,746 bp (23.26%) number of N's = 26,542 bp (0.04%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 720,447 number of insertions = 5,571 mapped reads with insertion percentage = 0.47% number of deletions = 29,319 mapped reads with deletion percentage = 2.45% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.0227X std coverageData = 0.2005X There is a 1.94% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.05% 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 5704841 0.022887971059458265 0.2459408969049392 chr2 243199373 6101099 0.02508682043353788 0.2322848713293891 chr3 198022430 5666498 0.028615435130252668 0.19965267829335762 chr4 191154276 3809326 0.019928018769509503 0.167755383475072 chr5 180915260 3912549 0.021626417804667224 0.17066087781046663 chr6 171115067 4145785 0.02422805351208494 0.19579002131889847 chr7 159138663 3933987 0.024720497997397402 0.2414312475737796 chr8 146364022 5298355 0.03619984561506515 0.262370364438056 chr9 141213431 2726263 0.019305975222710933 0.1832632765412489 chr10 135534747 3530832 0.026051120307916315 0.20938763046718692 chr11 135006516 3019832 0.022368046294891426 0.2031099443549003 chr12 133851895 3094259 0.023117035436816192 0.17740646261692797 chr13 115169878 2160460 0.018758898051450573 0.16196008350671218 chr14 107349540 2379613 0.02216696038008174 0.17542126056407295 chr15 102531392 1964237 0.019157420587833235 0.16171867939211898 chr16 90354753 1716939 0.01900219903207527 0.16937820154377847 chr17 81195210 1680821 0.02070098716414429 0.1766497893301852 chr18 78077248 1397166 0.017894662475808575 0.2523420264917376 chr19 59128983 1112512 0.018815003126301022 0.1877598123284359 chr20 63025520 1497148 0.023754631457225582 0.181348023660516 chr21 48129895 826569 0.017173712928316175 0.15705100328935967 chr22 51304566 745929 0.014539232239095444 0.13779090794874052 chrMT 16571 42517 2.5657473900187076 2.9772996798767695 chrX 155270560 3604538 0.023214561730182465 0.18509225839018 chrY 59373566 175406 0.002954277666259763 0.07183630026317118