BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524359.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 = 2,598,534
number of mapped reads = 2,363,437 (90.95%)
number of supplementary alignments = 10,059 (0.39%)
number of secondary alignments = 0
number of mapped bases = 136,546,306 bp
number of sequenced bases = 136,509,581 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 129,082
duplication rate = 3.97%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.3671
>>>>>>> ACTG content
number of A's = 34,105,477 bp (24.98%)
number of C's = 27,067,128 bp (19.83%)
number of T's = 42,466,836 bp (31.11%)
number of G's = 32,851,889 bp (24.07%)
number of N's = 18,251 bp (0.01%)
GC percentage = 43.89%
>>>>>>> Mismatches and indels
general error rate = 0.0054
number of mismatches = 717,159
number of insertions = 8,319
mapped reads with insertion percentage = 0.35%
number of deletions = 23,033
mapped reads with deletion percentage = 0.97%
homopolymer indels = 42.5%
>>>>>>> Coverage
mean coverageData = 0.0441X
std coverageData = 0.4131X
There is a 3.79% of reference with a coverageData >= 1X
There is a 0.44% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 11006413 0.04415801636056907 0.8063480369238305
chr2 243199373 11221941 0.046142968468919535 0.6038260695230838
chr3 198022430 9012472 0.04551237958245437 0.2478807151771875
chr4 191154276 8454392 0.04422810819047542 0.29566159798736463
chr5 180915260 8240821 0.04555072358185816 0.2448048938177067
chr6 171115067 7520359 0.043949133947392256 0.267227717168412
chr7 159138663 7544134 0.047406041107684815 0.5106860450686515
chr8 146364022 6997888 0.04781153116986632 0.33190596770893416
chr9 141213431 5603944 0.03968421389039121 0.31788969876847245
chr10 135534747 6614590 0.048803647377598305 0.41513103259578177
chr11 135006516 6253997 0.04632366781467052 0.3564042023460938
chr12 133851895 6168431 0.04608400202328103 0.2510581908344346
chr13 115169878 4140957 0.03595520870483166 0.21737201509238524
chr14 107349540 4151901 0.03867646754704305 0.24533415674635883
chr15 102531392 3892770 0.03796661611694495 0.22523827027266194
chr16 90354753 4263448 0.047185652756972285 0.28067021679501003
chr17 81195210 3975464 0.04896180452024202 0.2693768893208525
chr18 78077248 3659179 0.04686613698269693 0.6424505992284619
chr19 59128983 3049280 0.051569972038923786 0.5160922060313902
chr20 63025520 3022975 0.04796430081021148 0.2587090394286325
chr21 48129895 1833705 0.03809908581766073 0.26758266171014794
chr22 51304566 1746796 0.03404757385531728 0.214107678855311
chrMT 16571 29646 1.7890290266127573 1.7081597230457832
chrX 155270560 7663528 0.049355962907585316 0.2946036103388597
chrY 59373566 477275 0.00803850993218093 0.22255764219096055