BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525034.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 = 542,170 number of mapped reads = 500,794 (92.37%) number of supplementary alignments = 2,004 (0.37%) number of secondary alignments = 0 number of mapped bases = 29,353,353 bp number of sequenced bases = 29,343,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,352 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.712 >>>>>>> ACTG content number of A's = 7,798,012 bp (26.57%) number of C's = 5,542,066 bp (18.89%) number of T's = 8,887,018 bp (30.29%) number of G's = 7,116,481 bp (24.25%) number of N's = 320 bp (0%) GC percentage = 43.14% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 143,840 number of insertions = 2,332 mapped reads with insertion percentage = 0.46% number of deletions = 5,774 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.98% >>>>>>> Coverage mean coverageData = 0.0095X std coverageData = 0.1174X There is a 0.9% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2304464 0.00924556974323446 0.1685128976924574 chr2 243199373 2496817 0.010266543738169917 0.1311139170754119 chr3 198022430 1907008 0.00963026259197001 0.10144327020613844 chr4 191154276 1948734 0.01019456138140483 0.10934640205489524 chr5 180915260 1748310 0.009663695588752436 0.10182732035017887 chr6 171115067 1652075 0.009654760559454417 0.10898788859729466 chr7 159138663 1586256 0.009967760003111248 0.1300323070603649 chr8 146364022 1488981 0.010173135307801257 0.12848740590629115 chr9 141213431 1216608 0.008615384467218278 0.10419043380753208 chr10 135534747 1554533 0.011469627047003673 0.1314684416385747 chr11 135006516 1356474 0.010047470597641377 0.11564771296045731 chr12 133851895 1303111 0.009735469191526949 0.10235109499389287 chr13 115169878 911253 0.007912251153031525 0.09224212323277028 chr14 107349540 875686 0.008157333510697857 0.09382260766473755 chr15 102531392 850530 0.008295313107618787 0.09445497044523397 chr16 90354753 867497 0.009601011249513349 0.10352026354708316 chr17 81195210 793408 0.009771610911530372 0.10528018469825176 chr18 78077248 742959 0.009515691434206287 0.1456086022154919 chr19 59128983 595751 0.010075448109770466 0.1306559543510332 chr20 63025520 684905 0.010867105896151273 0.10860361544554087 chr21 48129895 385106 0.008001388741861997 0.09677469307879331 chr22 51304566 356267 0.006944157757810484 0.0859243032458275 chrMT 16571 1473 0.0888902299197393 0.3010717174819666 chrX 155270560 1631980 0.010510556540789187 0.1090330779545297 chrY 59373566 93167 0.0015691663188968639 0.0591144441053834