BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751187.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 = 5,091,818 number of mapped reads = 4,885,633 (95.95%) number of supplementary alignments = 159,571 (3.13%) number of secondary alignments = 0 number of mapped bases = 478,134,376 bp number of sequenced bases = 477,994,348 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,237 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2586 >>>>>>> ACTG content number of A's = 139,778,791 bp (29.24%) number of C's = 99,375,978 bp (20.79%) number of T's = 140,525,168 bp (29.4%) number of G's = 98,311,904 bp (20.57%) number of N's = 2,507 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 1,785,799 number of insertions = 129,184 mapped reads with insertion percentage = 2.58% number of deletions = 63,593 mapped reads with deletion percentage = 1.27% homopolymer indels = 48.69% >>>>>>> Coverage mean coverageData = 0.1545X std coverageData = 1.4785X There is a 12.4% of reference with a coverageData >= 1X There is a 2.14% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 57365487 0.23015183179824455 4.228651753470273 chr2 243199373 35817277 0.14727536735878016 0.6140864663591041 chr3 198022430 31512256 0.15913478084275604 0.49286391636434074 chr4 191154276 22323262 0.11678138970848866 0.44136756084203754 chr5 180915260 38864145 0.21481960670426586 0.5377757381836973 chr6 171115067 26909925 0.15726215973722524 1.124603553255995 chr7 159138663 27060963 0.17004643931185975 0.7747946674994409 chr8 146364022 23710422 0.16199624522479986 0.5820982936325321 chr9 141213431 21058976 0.14912870433691255 0.7308415602266527 chr10 135534747 23732568 0.17510320065746682 1.8402482635175783 chr11 135006516 21577800 0.1598278411984204 0.7279654212908114 chr12 133851895 25605661 0.19129845714922453 0.5070060682923782 chr13 115169878 13912586 0.1208005621053102 0.39241046491758835 chr14 107349540 10203607 0.09505030948432569 0.3794455736474105 chr15 102531392 11325395 0.11045782934459722 0.37716942063615905 chr16 90354753 13657633 0.151155667483259 1.0683542133559385 chr17 81195210 12542256 0.1544703930194897 0.7348354045979842 chr18 78077248 9976972 0.12778334605236086 1.6908213722958885 chr19 59128983 8898293 0.1504895323499814 3.017477860516555 chr20 63025520 8523206 0.13523420354167645 0.43332578117586784 chr21 48129895 5986743 0.1243872025899911 0.4465625299204392 chr22 51304566 5358444 0.10444380330592798 0.37520000231594797 chrMT 16571 271783 16.401122442821798 8.376028764252808 chrX 155270560 20739886 0.13357255876452045 0.48547302123558855 chrY 59373566 1198830 0.02019130870461781 0.8926529777063996