BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714138.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 674,708
number of mapped reads = 573,492 (85%)
number of supplementary alignments = 17,610 (2.61%)
number of secondary alignments = 0
number of mapped bases = 72,868,147 bp
number of sequenced bases = 72,306,830 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 572,391
duplication rate = 31.13%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 17.4681
>>>>>>> ACTG content
number of A's = 20,336,598 bp (28.13%)
number of C's = 14,793,438 bp (20.46%)
number of T's = 19,266,152 bp (26.64%)
number of G's = 17,910,117 bp (24.77%)
number of N's = 525 bp (0%)
GC percentage = 45.23%
>>>>>>> Mismatches and indels
general error rate = 0.0355
number of mismatches = 2,092,797
number of insertions = 96,690
mapped reads with insertion percentage = 16.46%
number of deletions = 147,846
mapped reads with deletion percentage = 24.12%
homopolymer indels = 20.52%
>>>>>>> Coverage
mean coverageData = 0.0235X
std coverageData = 54.1467X
There is a 0.02% of reference with a coverageData >= 1X
There is a 0.01% 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 1149364 0.004611278380726683 3.6145219137837694
chr2 243199373 4512814 0.018556026458176764 14.260738788411135
chr3 198022430 39154565 0.1977279291037889 197.06169913289298
chr4 191154276 275730 0.0014424474606050664 1.0300967411378383
chr5 180915260 13370470 0.07390460041900279 68.19038699516798
chr6 171115067 9866276 0.057658721543205775 51.895973675254275
chr7 159138663 330559 0.002077175928014426 0.9556264722868436
chr8 146364022 1577537 0.01077817470744279 10.779919093652712
chr9 141213431 244812 0.0017336311303136598 1.2056287666810657
chr10 135534747 1521475 0.011225719113933197 10.072357602014684
chr11 135006516 167348 0.0012395549856275086 0.7835969729806991
chr12 133851895 97969 7.319209040708763E-4 0.3377560333967612
chr13 115169878 27372 2.3766631063028477E-4 0.04284550281163594
chr14 107349540 53114 4.947762235404082E-4 0.1639192967783181
chr15 102531392 150103 0.001463971151391371 0.37162899376869035
chr16 90354753 27661 3.0613774130952467E-4 0.04762247558872741
chr17 81195210 25510 3.141810951655892E-4 0.05798484762675476
chr18 78077248 43625 5.58741517119046E-4 0.28640459627004194
chr19 59128983 16238 2.746199778203525E-4 0.03545810927671279
chr20 63025520 82007 0.0013011713350401552 0.6146341556522893
chr21 48129895 20739 4.308964314175213E-4 0.20286481343201834
chr22 51304566 10021 1.9532374564868165E-4 0.05932514772800716
chrMT 16571 1488 0.08979542574376924 0.8365367641741157
chrX 155270560 130034 8.374671927505124E-4 0.1062286523733735
chrY 59373566 11316 1.9058986620409493E-4 0.04903761178552382