BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524869.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 = 1,411,124
number of mapped reads = 1,299,996 (92.12%)
number of supplementary alignments = 5,349 (0.38%)
number of secondary alignments = 0
number of mapped bases = 75,851,316 bp
number of sequenced bases = 75,829,724 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 37,291
duplication rate = 1.96%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.5812
>>>>>>> ACTG content
number of A's = 20,031,609 bp (26.42%)
number of C's = 13,647,312 bp (18%)
number of T's = 24,784,785 bp (32.68%)
number of G's = 17,355,970 bp (22.89%)
number of N's = 10,048 bp (0.01%)
GC percentage = 40.89%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 362,150
number of insertions = 6,034
mapped reads with insertion percentage = 0.46%
number of deletions = 13,952
mapped reads with deletion percentage = 1.07%
homopolymer indels = 42.76%
>>>>>>> Coverage
mean coverageData = 0.0245X
std coverageData = 0.2571X
There is a 2.25% of reference with a coverageData >= 1X
There is a 0.13% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 6295964 0.025259571971136634 0.5007689883949672
chr2 243199373 4914305 0.020206898313014976 0.24668167530090676
chr3 198022430 5485957 0.027703715180143987 0.17514745641282925
chr4 191154276 4149197 0.02170601195444877 0.1656951621258688
chr5 180915260 4628023 0.025581164352857795 0.17069842227666035
chr6 171115067 5060198 0.02957190204647496 0.20178518735510229
chr7 159138663 3461625 0.021752256395417877 0.35512576510838123
chr8 146364022 8323524 0.05686864767900406 0.3538589275852617
chr9 141213431 3130961 0.022171835765395432 0.21256639168196745
chr10 135534747 3768361 0.027803652446409186 0.23630410689162826
chr11 135006516 3663824 0.02713812717009896 0.23243686606228894
chr12 133851895 3005747 0.022455767249316867 0.1627997928773764
chr13 115169878 1990682 0.017284745235208114 0.13989510410732187
chr14 107349540 1581593 0.014733113900627799 0.1381065237797629
chr15 102531392 2239614 0.021843202909017367 0.15702839398469062
chr16 90354753 2104141 0.023287551901115817 0.17495747720799404
chr17 81195210 1988731 0.02449320594158202 0.1837422164863008
chr18 78077248 1855743 0.02376803803330773 0.37579815759176666
chr19 59128983 1057021 0.01787652934940552 0.3500308222750804
chr20 63025520 1577128 0.025023641217081588 0.16973830590752956
chr21 48129895 1110058 0.023063794342372865 0.16827442515121163
chr22 51304566 428319 0.008348555175381467 0.09578899620002508
chrMT 16571 1697 0.10240782089191962 0.3630726947071569
chrX 155270560 3849078 0.024789490035973336 0.1911803126371968
chrY 59373566 179825 0.0030287047269486897 0.08471159774631845