BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524961.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 = 1,366,105
number of mapped reads = 1,269,723 (92.94%)
number of supplementary alignments = 3,072 (0.22%)
number of secondary alignments = 0
number of mapped bases = 74,168,629 bp
number of sequenced bases = 74,144,762 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 36,058
duplication rate = 2.01%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9128
>>>>>>> ACTG content
number of A's = 18,567,833 bp (25.04%)
number of C's = 13,098,650 bp (17.67%)
number of T's = 23,086,496 bp (31.14%)
number of G's = 19,391,019 bp (26.15%)
number of N's = 764 bp (0%)
GC percentage = 43.82%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 353,066
number of insertions = 4,639
mapped reads with insertion percentage = 0.36%
number of deletions = 14,167
mapped reads with deletion percentage = 1.11%
homopolymer indels = 42.96%
>>>>>>> Coverage
mean coverageData = 0.024X
std coverageData = 0.2326X
There is a 2.2% of reference with a coverageData >= 1X
There is a 0.14% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 8014951 0.0321561927021237 0.4386237435377897
chr2 243199373 6819007 0.028038752386092707 0.2570714594400739
chr3 198022430 4168775 0.02105203435792602 0.15477697145849492
chr4 191154276 4947655 0.02588304642476321 0.1821706558047474
chr5 180915260 3275862 0.018107162436159337 0.14602232944521645
chr6 171115067 4407031 0.025754780553602565 0.23784881763849952
chr7 159138663 4857605 0.0305243547257903 0.31493070916887395
chr8 146364022 4496859 0.030723800415924617 0.23331806644373929
chr9 141213431 1904122 0.013484000682626287 0.170784673999882
chr10 135534747 3856945 0.028457241300638574 0.2293264348851606
chr11 135006516 3189902 0.023627763270329855 0.21010285137073687
chr12 133851895 3961781 0.029598243640853946 0.18499874846913267
chr13 115169878 1498021 0.013007055542769612 0.12503403926972365
chr14 107349540 1877225 0.017487033479603172 0.14401698763419601
chr15 102531392 2164787 0.02111340690663792 0.16335848463963598
chr16 90354753 2322694 0.0257063842562881 0.1776353593518813
chr17 81195210 1897298 0.023367117345961665 0.20178070956190636
chr18 78077248 1522997 0.019506284340349702 0.2734663250287795
chr19 59128983 1741315 0.029449432607356024 0.27961049083766737
chr20 63025520 1433067 0.022737884590242174 0.16174697139293645
chr21 48129895 1066652 0.02216194321637311 0.16501490655881337
chr22 51304566 1090408 0.021253624872296942 0.15501323284345656
chrMT 16571 65997 3.982680586566894 3.076357567751852
chrX 155270560 3401589 0.02190749489149778 0.17688454362519251
chrY 59373566 186084 0.0031341220097846237 0.07972927426289207