BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717053.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 = 1,084,000 number of mapped reads = 928,668 (85.67%) number of supplementary alignments = 3,646 (0.34%) number of secondary alignments = 0 number of mapped bases = 52,201,889 bp number of sequenced bases = 52,187,261 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,823 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.4641 >>>>>>> ACTG content number of A's = 12,403,075 bp (23.77%) number of C's = 11,739,774 bp (22.5%) number of T's = 14,737,893 bp (28.24%) number of G's = 13,305,081 bp (25.49%) number of N's = 1,438 bp (0%) GC percentage = 47.99% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 270,198 number of insertions = 4,587 mapped reads with insertion percentage = 0.49% number of deletions = 8,786 mapped reads with deletion percentage = 0.94% homopolymer indels = 33.27% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 0.1597X There is a 1.53% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5659186 0.022704802007293697 0.19964220926223533 chr2 243199373 4271174 0.017562438370266685 0.19277341030090406 chr3 198022430 4193669 0.02117774738952552 0.16221784414312865 chr4 191154276 3058145 0.015998308089116457 0.15319146763242766 chr5 180915260 3229795 0.017852529410730747 0.14554179827089694 chr6 171115067 3302441 0.019299533687468912 0.15606139645220368 chr7 159138663 2488018 0.015634277384874096 0.15229518462702926 chr8 146364022 2844628 0.019435295376072678 0.15743377787026475 chr9 141213431 2072597 0.014677052921403772 0.1401556469177014 chr10 135534747 1794353 0.013239062599939778 0.18535697119364822 chr11 135006516 2536015 0.018784389636423177 0.18519128029608534 chr12 133851895 2409912 0.018004317383777047 0.14593327174950374 chr13 115169878 1241585 0.010780466399382658 0.1121969360444177 chr14 107349540 1509037 0.014057228377503993 0.13325315869410104 chr15 102531392 1092191 0.010652259553834986 0.11197194651807951 chr16 90354753 1443457 0.015975440716439124 0.14566005187023476 chr17 81195210 1561856 0.019235814526497315 0.15955366482126998 chr18 78077248 1209957 0.015496921715273572 0.17359958043218093 chr19 59128983 1525559 0.025800528312824186 0.2020064061825033 chr20 63025520 1524738 0.024192390637951103 0.17630405242822128 chr21 48129895 927442 0.019269562088178253 0.16282248066718683 chr22 51304566 594875 0.011594971878331453 0.12120001062790568 chrMT 16571 7296 0.44028724880815884 0.7327631953574365 chrX 155270560 1543198 0.009938767529401581 0.11574649411976129 chrY 59373566 160765 0.0027076864475345814 0.09098998697030948