BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867857.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 = 3,118,527 number of mapped reads = 2,871,312 (92.07%) number of supplementary alignments = 12,716 (0.41%) number of secondary alignments = 0 number of mapped bases = 169,430,626 bp number of sequenced bases = 169,378,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,084 duplication rate = 5.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8481 >>>>>>> ACTG content number of A's = 43,817,774 bp (25.87%) number of C's = 28,902,169 bp (17.06%) number of T's = 54,264,498 bp (32.04%) number of G's = 42,370,057 bp (25.01%) number of N's = 24,401 bp (0.01%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 852,560 number of insertions = 12,803 mapped reads with insertion percentage = 0.44% number of deletions = 32,673 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.71% >>>>>>> Coverage mean coverageData = 0.0547X std coverageData = 0.4869X There is a 4.58% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13576226 0.05446817322071988 0.930888420776791 chr2 243199373 14225230 0.05849205047087025 0.6807261230933064 chr3 198022430 11299086 0.05705962703315983 0.27744207480023936 chr4 191154276 10924236 0.05714879221430547 0.3420864989589362 chr5 180915260 10232594 0.05656014865744327 0.2815502281572076 chr6 171115067 9684288 0.056595179897279295 0.3335375570984028 chr7 159138663 9411922 0.059142899799277567 0.5783147630773142 chr8 146364022 8587918 0.058675061553036575 0.5518152310049977 chr9 141213431 7164500 0.05073525902787533 0.3991003946323608 chr10 135534747 8281270 0.06110071537596186 0.4907789437160283 chr11 135006516 7591936 0.056233848742530325 0.4086709833469344 chr12 133851895 7678070 0.05736243031897307 0.2829732322852606 chr13 115169878 5343910 0.04640024017391075 0.25211456395353166 chr14 107349540 5081759 0.047338432935995815 0.26927547790902473 chr15 102531392 4889295 0.04768583459785663 0.25840050601774206 chr16 90354753 4963453 0.054932948574382134 0.30694997655713135 chr17 81195210 4624622 0.05695683279838799 0.31075955040406755 chr18 78077248 4450503 0.057001279040982594 0.7561187986505813 chr19 59128983 3579084 0.06053011261837532 0.6850526995737407 chr20 63025520 3577121 0.05675670744168394 0.2871567570966415 chr21 48129895 2219859 0.04612224896813093 0.3176347439770406 chr22 51304566 2043996 0.03984043057688082 0.23215812446757342 chrMT 16571 51660 3.1174944179590853 2.577013625679758 chrX 155270560 9390872 0.06048069898118484 0.33164272622623153 chrY 59373566 557216 0.009384917186884143 0.3419806987376476