BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524397.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 = 540,299
number of mapped reads = 492,989 (91.24%)
number of supplementary alignments = 1,813 (0.34%)
number of secondary alignments = 0
number of mapped bases = 28,657,408 bp
number of sequenced bases = 28,649,462 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 9,123
duplication rate = 1.35%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.6909
>>>>>>> ACTG content
number of A's = 7,637,626 bp (26.66%)
number of C's = 5,023,080 bp (17.53%)
number of T's = 9,001,771 bp (31.42%)
number of G's = 6,983,397 bp (24.38%)
number of N's = 3,588 bp (0.01%)
GC percentage = 41.91%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 141,326
number of insertions = 2,361
mapped reads with insertion percentage = 0.48%
number of deletions = 5,153
mapped reads with deletion percentage = 1.04%
homopolymer indels = 43.73%
>>>>>>> Coverage
mean coverageData = 0.0093X
std coverageData = 0.1209X
There is a 0.88% 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 2305178 0.009248434329878761 0.18970875575407323
chr2 243199373 2416485 0.009936230386580808 0.13535493982879587
chr3 198022430 1896875 0.00957909162108555 0.10048287259307147
chr4 191154276 1889258 0.009883420028752064 0.10590336815722473
chr5 180915260 1712717 0.009466957071504084 0.1002266205667742
chr6 171115067 1675979 0.009794456031157093 0.10659194155053511
chr7 159138663 1597382 0.010037673874387143 0.1517590265064853
chr8 146364022 1465830 0.01001496119039418 0.11798771519248903
chr9 141213431 1186312 0.008400843967880081 0.10916243255248533
chr10 135534747 1346275 0.009933061667204795 0.11643902705205866
chr11 135006516 1326026 0.009821940742474979 0.11752199954783057
chr12 133851895 1312926 0.009808796506018836 0.10289551897548353
chr13 115169878 912403 0.007922236402820537 0.09141687988757345
chr14 107349540 883696 0.0082319495733284 0.09572386504063449
chr15 102531392 821025 0.008007547581134956 0.09207273162432579
chr16 90354753 814316 0.009012431255276631 0.09953525521245814
chr17 81195210 753597 0.009281298736711192 0.1019885643769538
chr18 78077248 769554 0.009856315632436226 0.1696759885211871
chr19 59128983 559831 0.009467962606426022 0.14028312474530302
chr20 63025520 596298 0.009461215076051733 0.10165263887868894
chr21 48129895 374587 0.007782834348589375 0.09457963012081294
chr22 51304566 325058 0.0063358493277187065 0.08174618819230328
chrMT 16571 1200 0.07241566592239454 0.2871376212396543
chrX 155270560 1628663 0.010489193830433792 0.11034109501115576
chrY 59373566 85937 0.001447394956873569 0.05008914656591224