BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524341.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 = 574,585
number of mapped reads = 515,923 (89.79%)
number of supplementary alignments = 2,194 (0.38%)
number of secondary alignments = 0
number of mapped bases = 29,365,553 bp
number of sequenced bases = 29,357,931 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 8,840
duplication rate = 1.17%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.3039
>>>>>>> ACTG content
number of A's = 7,296,375 bp (24.85%)
number of C's = 5,715,918 bp (19.47%)
number of T's = 9,246,556 bp (31.5%)
number of G's = 7,095,260 bp (24.17%)
number of N's = 3,822 bp (0.01%)
GC percentage = 43.64%
>>>>>>> Mismatches and indels
general error rate = 0.0054
number of mismatches = 154,624
number of insertions = 1,881
mapped reads with insertion percentage = 0.36%
number of deletions = 4,850
mapped reads with deletion percentage = 0.93%
homopolymer indels = 42.15%
>>>>>>> Coverage
mean coverageData = 0.0095X
std coverageData = 0.122X
There is a 0.9% 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 2457524 0.009859650460008283 0.17560499783179068
chr2 243199373 1898725 0.00780727752945317 0.1534398028660912
chr3 198022430 2040605 0.010304918488274284 0.10493962252790698
chr4 191154276 1539118 0.008051705837854237 0.09675132023766328
chr5 180915260 1749787 0.0096718596319625 0.10172784215834342
chr6 171115067 1883510 0.011007271498774564 0.1124521455296938
chr7 159138663 1361399 0.00855479727135825 0.14172499266121616
chr8 146364022 2997813 0.020481898208563852 0.1653069231954475
chr9 141213431 1213870 0.008595995376672067 0.10553674684848408
chr10 135534747 1489975 0.010993306388065933 0.1260874015237408
chr11 135006516 1401710 0.010382535906637277 0.11322906982826957
chr12 133851895 1186114 0.008861391166707054 0.09810301567534324
chr13 115169878 732896 0.006363608373363042 0.08276289446121937
chr14 107349540 625674 0.0058283808202624805 0.0820457514378342
chr15 102531392 884318 0.008624851206545601 0.09647063277348654
chr16 90354753 926976 0.010259294273097066 0.1079544924300989
chr17 81195210 895128 0.011024394173006019 0.1130858952040834
chr18 78077248 686583 0.008793637296232571 0.14086648617434588
chr19 59128983 534603 0.009041302130970187 0.14562112013311107
chr20 63025520 651730 0.010340731817841408 0.1057408980136064
chr21 48129895 414867 0.008619736236698625 0.09811964892042158
chr22 51304566 207430 0.004043109925147793 0.06558765247810165
chrMT 16571 18606 1.1228049001267275 1.250691169909206
chrX 155270560 1478556 0.00952244907212288 0.10659337443655449
chrY 59373566 88036 0.0014827473896380082 0.04881121937465935