BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716185.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 = 536,881
number of mapped reads = 478,693 (89.16%)
number of supplementary alignments = 2,267 (0.42%)
number of secondary alignments = 0
number of mapped bases = 27,148,608 bp
number of sequenced bases = 27,140,647 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 11,125
duplication rate = 1.76%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.4406
>>>>>>> ACTG content
number of A's = 6,812,685 bp (25.1%)
number of C's = 5,233,780 bp (19.28%)
number of T's = 8,504,198 bp (31.33%)
number of G's = 6,589,614 bp (24.28%)
number of N's = 370 bp (0%)
GC percentage = 43.56%
>>>>>>> Mismatches and indels
general error rate = 0.0057
number of mismatches = 152,008
number of insertions = 1,815
mapped reads with insertion percentage = 0.38%
number of deletions = 4,713
mapped reads with deletion percentage = 0.98%
homopolymer indels = 41.8%
>>>>>>> Coverage
mean coverageData = 0.0088X
std coverageData = 0.1189X
There is a 0.83% 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 1863875 0.007477915170369827 0.17575374442412828
chr2 243199373 2123942 0.00873333666037042 0.12843607575009933
chr3 198022430 1642789 0.008295974349976414 0.09391208798594161
chr4 191154276 1643555 0.00859805511230102 0.09984809841657481
chr5 180915260 1503023 0.008307884033663053 0.09500011634146052
chr6 171115067 1431488 0.008365645557091708 0.09851183390310507
chr7 159138663 1734525 0.01089945690947523 0.14563604649751746
chr8 146364022 1179763 0.008060471308994227 0.10782660758372298
chr9 141213431 1264206 0.00895244872281306 0.12259796231382458
chr10 135534747 1057624 0.00780334212008379 0.11869522876366256
chr11 135006516 1009130 0.007474676259329587 0.10287592998674391
chr12 133851895 1992642 0.014886916617803581 0.13049996815733209
chr13 115169878 1017887 0.008838135610424108 0.09663769597605269
chr14 107349540 957165 0.008916340023441181 0.10008075348226916
chr15 102531392 652011 0.006359135356320921 0.08208267232164136
chr16 90354753 784045 0.00867740737446319 0.09988858407814466
chr17 81195210 849970 0.010468228359776396 0.1069525178589851
chr18 78077248 848160 0.010863087797356792 0.18323491234323705
chr19 59128983 482609 0.008161970247315095 0.148567477380373
chr20 63025520 1003768 0.015926373951377155 0.131717130223472
chr21 48129895 332226 0.006902695299875472 0.09028443458043668
chr22 51304566 263958 0.005144922188796997 0.0737104980399031
chrMT 16571 2688 0.1622110916661638 0.42760746424688884
chrX 155270560 1420901 0.009151129486491194 0.1062075348030951
chrY 59373566 86658 0.0014595384080518256 0.04850195032350171