BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714169.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 887,840
number of mapped reads = 764,490 (86.11%)
number of supplementary alignments = 40,344 (4.54%)
number of secondary alignments = 0
number of mapped bases = 99,747,356 bp
number of sequenced bases = 98,086,277 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 753,517
duplication rate = 39.31%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 40.8635
>>>>>>> ACTG content
number of A's = 30,229,053 bp (30.82%)
number of C's = 18,744,001 bp (19.11%)
number of T's = 27,603,249 bp (28.14%)
number of G's = 21,509,262 bp (21.93%)
number of N's = 712 bp (0%)
GC percentage = 41.04%
>>>>>>> Mismatches and indels
general error rate = 0.0371
number of mismatches = 3,451,727
number of insertions = 83,452
mapped reads with insertion percentage = 10%
number of deletions = 299,816
mapped reads with deletion percentage = 37.79%
homopolymer indels = 26.37%
>>>>>>> Coverage
mean coverageData = 0.0322X
std coverageData = 20.0175X
There is a 0.04% of reference with a coverageData >= 1X
There is a 0.02% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0.01% 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 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% 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 2502161 0.010038735269590362 6.091580095853972
chr2 243199373 13809900 0.05678427468643186 26.198204751734487
chr3 198022430 8474177 0.04279402590908515 25.860920882924386
chr4 191154276 3594781 0.018805653084108878 7.189945055508031
chr5 180915260 6712876 0.03710508444671831 17.85617120403858
chr6 171115067 1068111 0.006242062833660346 1.4626059985745614
chr7 159138663 2321504 0.014587932035095707 3.6022667308676835
chr8 146364022 22303763 0.1523855568822781 69.07531686991217
chr9 141213431 2213030 0.015671526315368684 7.02272785085229
chr10 135534747 2431829 0.017942476404224226 4.6494682676831784
chr11 135006516 3746607 0.02775130498145734 8.86273771055304
chr12 133851895 2063943 0.015419602389641178 5.112262379859402
chr13 115169878 1048960 0.009107937059723204 2.410134840725227
chr14 107349540 3620940 0.03373037276172772 12.219788400647301
chr15 102531392 1523999 0.01486373070990785 3.2572205967871115
chr16 90354753 861730 0.00953718505544473 3.576049410661949
chr17 81195210 1100071 0.013548471640137392 3.8831192151160416
chr18 78077248 914165 0.011708468515693586 2.139614516184159
chr19 59128983 109626 0.0018540146377961548 0.37227738389728077
chr20 63025520 1232417 0.019554253578550403 10.37501181415058
chr21 48129895 446757 0.009282318193297534 2.65899291848739
chr22 51304566 3663375 0.07140446329864675 23.612380661325155
chrMT 16571 32363 1.9529901635387121 13.932996908670896
chrX 155270560 13926150 0.08968957154530775 23.150929415630568
chrY 59373566 24121 4.062582328304148E-4 0.14869429941308054