BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751175.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,396,861 number of mapped reads = 3,692,652 (83.98%) number of supplementary alignments = 221,563 (5.04%) number of secondary alignments = 0 number of mapped bases = 362,672,254 bp number of sequenced bases = 362,544,164 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,569 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9411 >>>>>>> ACTG content number of A's = 106,526,149 bp (29.38%) number of C's = 74,515,127 bp (20.55%) number of T's = 107,143,211 bp (29.55%) number of G's = 74,357,664 bp (20.51%) number of N's = 2,013 bp (0%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,639,039 number of insertions = 257,654 mapped reads with insertion percentage = 6.69% number of deletions = 57,907 mapped reads with deletion percentage = 1.53% homopolymer indels = 52.79% >>>>>>> Coverage mean coverageData = 0.1172X std coverageData = 1.5924X There is a 8.84% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 42786368 0.17166002567351676 4.551846168669615 chr2 243199373 27317048 0.11232367774237642 0.6624962015493211 chr3 198022430 23954537 0.1209688064124857 0.5217987288299212 chr4 191154276 16934914 0.0885929122506263 0.6169065414752654 chr5 180915260 29704877 0.1641922135258242 0.5000953580620434 chr6 171115067 18241847 0.10660573215332347 0.9279636870801727 chr7 159138663 20577261 0.12930397058821588 0.9798992902993097 chr8 146364022 17950669 0.12264399921997224 0.5907292562875437 chr9 141213431 15662522 0.11091382660336324 0.7229281405368013 chr10 135534747 19051968 0.14056888304812346 2.359505770345959 chr11 135006516 16548306 0.12257412819985666 0.7433651287633035 chr12 133851895 19259488 0.14388655461321634 0.4692279617860457 chr13 115169878 10454552 0.09077505491496657 0.36472746102867665 chr14 107349540 8143176 0.0758566454965713 0.42323780509415654 chr15 102531392 9017020 0.08794399280173627 0.3632929977283744 chr16 90354753 11047926 0.1222727707528568 1.120636809370132 chr17 81195210 9776461 0.12040686882883855 0.7216770397195685 chr18 78077248 7565184 0.09689357903598242 1.5480257394664245 chr19 59128983 6449669 0.10907796266342007 3.1940361271610898 chr20 63025520 6554219 0.10399309676461217 0.4313070429191517 chr21 48129895 4585579 0.0952750676061105 0.4969404032770967 chr22 51304566 4122514 0.08035374473297367 0.35252264258202787 chrMT 16571 511344 30.857763562850764 11.644206116413084 chrX 155270560 15318340 0.09865579154219577 0.4593909445119443 chrY 59373566 1136465 0.01914092544146666 0.8801260976199163