BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525062.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 = 645,239
number of mapped reads = 535,914 (83.06%)
number of supplementary alignments = 1,512 (0.23%)
number of secondary alignments = 0
number of mapped bases = 30,789,341 bp
number of sequenced bases = 30,779,478 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 19,422
duplication rate = 3.02%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.9242
>>>>>>> ACTG content
number of A's = 7,619,893 bp (24.76%)
number of C's = 5,808,641 bp (18.87%)
number of T's = 10,401,543 bp (33.79%)
number of G's = 6,946,436 bp (22.57%)
number of N's = 2,965 bp (0.01%)
GC percentage = 41.44%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 156,089
number of insertions = 2,178
mapped reads with insertion percentage = 0.4%
number of deletions = 6,144
mapped reads with deletion percentage = 1.14%
homopolymer indels = 42.93%
>>>>>>> Coverage
mean coverageData = 0.0099X
std coverageData = 0.1307X
There is a 0.92% of reference with a coverageData >= 1X
There is a 0.05% of reference with a coverageData >= 2X
There is a 0.01% 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 2560069 0.010271063677710957 0.215124351521576
chr2 243199373 2534155 0.010420072094511526 0.1552653531228689
chr3 198022430 2139370 0.010803675119025658 0.10949967343833551
chr4 191154276 2143910 0.011215600534094252 0.11845131467614917
chr5 180915260 2047834 0.011319299433336911 0.11217262431894257
chr6 171115067 1864750 0.010897637669744184 0.11725502514397367
chr7 159138663 1759909 0.011058965601589853 0.14021739563740693
chr8 146364022 1144874 0.007822099887361664 0.12606731579325742
chr9 141213431 1388468 0.009832407513701725 0.11293060449574138
chr10 135534747 1282415 0.009461890979145002 0.1332924200830853
chr11 135006516 1499363 0.01110585654991645 0.1181739897244025
chr12 133851895 1428209 0.01067006933297433 0.11018120870344195
chr13 115169878 1058711 0.009192603295108119 0.10108342193238143
chr14 107349540 985435 0.009179685353099789 0.1019530379416656
chr15 102531392 904567 0.008822341941870837 0.0989716683380081
chr16 90354753 920440 0.010186957181986873 0.11171846651508906
chr17 81195210 866594 0.010672969501526014 0.1108844796969517
chr18 78077248 828866 0.01061597355480562 0.16528931357461782
chr19 59128983 635460 0.010747013862896983 0.15775697899603652
chr20 63025520 626505 0.009940497119262166 0.1069789108687309
chr21 48129895 445270 0.009251422634518525 0.10703216988783044
chr22 51304566 389906 0.007599830393263633 0.09196841575754622
chrMT 16571 9364 0.5650835797477521 0.848868285226276
chrX 155270560 1221914 0.007869579397407983 0.09965711452235039
chrY 59373566 102983 0.0017344924170463335 0.07563057091816118