BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525090.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 = 464,032
number of mapped reads = 404,076 (87.08%)
number of supplementary alignments = 1,465 (0.32%)
number of secondary alignments = 0
number of mapped bases = 23,763,801 bp
number of sequenced bases = 23,756,879 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 11,298
duplication rate = 2.42%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.0898
>>>>>>> ACTG content
number of A's = 6,115,409 bp (25.74%)
number of C's = 4,467,810 bp (18.81%)
number of T's = 7,203,643 bp (30.32%)
number of G's = 5,967,191 bp (25.12%)
number of N's = 2,826 bp (0.01%)
GC percentage = 43.92%
>>>>>>> Mismatches and indels
general error rate = 0.0047
number of mismatches = 108,878
number of insertions = 1,801
mapped reads with insertion percentage = 0.44%
number of deletions = 4,276
mapped reads with deletion percentage = 1.05%
homopolymer indels = 44.15%
>>>>>>> Coverage
mean coverageData = 0.0077X
std coverageData = 0.103X
There is a 0.72% 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 1716018 0.006884709025459158 0.13632154842197367
chr2 243199373 2017736 0.008296633231862815 0.11493095620472751
chr3 198022430 1599147 0.008075585174871351 0.09365549922123731
chr4 191154276 1349774 0.007061176073299035 0.09524403632335132
chr5 180915260 1425731 0.007880656391285068 0.09277035528571768
chr6 171115067 1375266 0.008037083023203329 0.09582153480544417
chr7 159138663 1330734 0.008362103683125703 0.11056209925390843
chr8 146364022 1228378 0.008392622607760806 0.10967231111762532
chr9 141213431 1023494 0.007247851657963045 0.09473021665092055
chr10 135534747 1149355 0.008480150112354583 0.11453770067693335
chr11 135006516 1094717 0.008108623438590179 0.09903825275881838
chr12 133851895 1107349 0.008272942269513629 0.0953915359578377
chr13 115169878 770744 0.006692235968158272 0.08552640095542088
chr14 107349540 725025 0.006753871511699072 0.08733257288772203
chr15 102531392 697850 0.006806208190365737 0.08609317024916362
chr16 90354753 713859 0.00790062477399501 0.09517426123058567
chr17 81195210 659944 0.00812786862673303 0.0945909114698243
chr18 78077248 635651 0.008141308976463925 0.12321877042764785
chr19 59128983 509366 0.008614489445894918 0.1180554722103504
chr20 63025520 533672 0.008467554095547327 0.09724694025164252
chr21 48129895 324792 0.006748238283087881 0.09128497783816615
chr22 51304566 319323 0.006224065904777364 0.08262503197009037
chrMT 16571 14745 0.889807495021423 1.0470083217136739
chrX 155270560 1358538 0.008749488634548623 0.09988542382110417
chrY 59373566 82593 0.0013910735966237904 0.053139298058671236