BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524466.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 = 1,221,867
number of mapped reads = 1,111,524 (90.97%)
number of supplementary alignments = 3,851 (0.32%)
number of secondary alignments = 0
number of mapped bases = 64,690,619 bp
number of sequenced bases = 64,669,814 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 58,416
duplication rate = 4.17%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.8615
>>>>>>> ACTG content
number of A's = 16,511,524 bp (25.53%)
number of C's = 11,817,313 bp (18.27%)
number of T's = 21,114,428 bp (32.65%)
number of G's = 15,225,125 bp (23.54%)
number of N's = 1,424 bp (0%)
GC percentage = 41.82%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 328,223
number of insertions = 5,525
mapped reads with insertion percentage = 0.49%
number of deletions = 13,208
mapped reads with deletion percentage = 1.18%
homopolymer indels = 44.25%
>>>>>>> Coverage
mean coverageData = 0.0209X
std coverageData = 0.2301X
There is a 1.85% of reference with a coverageData >= 1X
There is a 0.17% 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 5172474 0.020752100754043858 0.36788678265850633
chr2 243199373 5467360 0.022480979011405593 0.3353756918841785
chr3 198022430 4262532 0.021525500924314482 0.16159518585336172
chr4 191154276 4072088 0.02130262573880377 0.17927040488528753
chr5 180915260 4006180 0.022143958447728512 0.16446182478199178
chr6 171115067 3677623 0.02149210507570324 0.17656842016560745
chr7 159138663 3485506 0.02190232049392045 0.29731904809112636
chr8 146364022 3365448 0.022993683516021445 0.29937665888012865
chr9 141213431 2756347 0.019519014448420278 0.1890369965779511
chr10 135534747 3055358 0.022542986707312775 0.20776614531163587
chr11 135006516 2925560 0.021669768887303188 0.19631703813963083
chr12 133851895 3024508 0.0225959296280415 0.1679605355499028
chr13 115169878 2048093 0.017783234953153287 0.14818393476459987
chr14 107349540 1996694 0.01859993065643318 0.15312376853805484
chr15 102531392 1869981 0.018238131400771386 0.14939986881796133
chr16 90354753 1837343 0.02033476866457706 0.16791224747457786
chr17 81195210 1765732 0.0217467508243405 0.16830925966130023
chr18 78077248 1722464 0.02206102346230236 0.32317622239379484
chr19 59128983 1291248 0.02183781851955749 0.2620852003995538
chr20 63025520 1341922 0.021291724368160708 0.1645732133971346
chr21 48129895 853541 0.017734113070473144 0.15785218986833122
chr22 51304566 786131 0.015322827211909366 0.13601041357598434
chrMT 16571 4596 0.2773520004827711 0.5827406281172705
chrX 155270560 3686433 0.02374199590701547 0.18382030672738237
chrY 59373566 215457 0.003628837115830301 0.11199557740739728