BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR8751209.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,504,611
number of mapped reads = 4,062,169 (90.18%)
number of supplementary alignments = 195,888 (4.35%)
number of secondary alignments = 0
number of mapped bases = 400,542,260 bp
number of sequenced bases = 400,415,166 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 119,272
duplication rate = 1.4%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 50.9977
>>>>>>> ACTG content
number of A's = 118,735,303 bp (29.65%)
number of C's = 81,479,114 bp (20.35%)
number of T's = 119,356,067 bp (29.81%)
number of G's = 80,841,776 bp (20.19%)
number of N's = 2,906 bp (0%)
GC percentage = 40.54%
>>>>>>> Mismatches and indels
general error rate = 0.0044
number of mismatches = 1,472,394
number of insertions = 223,099
mapped reads with insertion percentage = 5.3%
number of deletions = 58,391
mapped reads with deletion percentage = 1.41%
homopolymer indels = 52.08%
>>>>>>> Coverage
mean coverageData = 0.1294X
std coverageData = 1.4431X
There is a 10.65% of reference with a coverageData >= 1X
There is a 1.6% of reference with a coverageData >= 2X
There is a 0.29% of reference with a coverageData >= 3X
There is a 0.07% of reference with a coverageData >= 4X
There is a 0.02% 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% 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 38029430 0.15257506620214198 4.236956065772023
chr2 243199373 31811903 0.13080585943780373 0.6083736837511393
chr3 198022430 26868407 0.13568365462437765 0.4501329209256115
chr4 191154276 23239250 0.12157326786663146 0.41516310604709217
chr5 180915260 35606680 0.19681413276027682 0.5213437637704733
chr6 171115067 21251066 0.12419167039218118 0.7837013714557012
chr7 159138663 24612454 0.15466042969080368 0.9458412008843811
chr8 146364022 28817206 0.19688722410210893 0.9588831396274442
chr9 141213431 17650691 0.12499300438355612 0.8342931518980858
chr10 135534747 17016829 0.1255532575716543 1.5953088876292083
chr11 135006516 18254526 0.13521218486965472 0.619425680246367
chr12 133851895 18329173 0.1369362234281405 0.4210585762510105
chr13 115169878 14226776 0.12352861917592724 0.39157108607771784
chr14 107349540 10733074 0.09998248711638634 0.37689809156091414
chr15 102531392 12778360 0.12462875760040398 0.3952274500739045
chr16 90354753 10119752 0.11200021763105257 0.6123914776877608
chr17 81195210 11385243 0.14022062385207207 0.7084443327448334
chr18 78077248 7109057 0.09105158265824123 1.5441308151168687
chr19 59128983 6320054 0.1068858904608591 2.827468976561518
chr20 63025520 7347185 0.11657476209636985 0.39525373929019614
chr21 48129895 1711395 0.035557837805380625 0.24559392923034204
chr22 51304566 3564462 0.06947650624312854 0.29900753900763677
chrMT 16571 323516 19.523022147124493 8.700815175265006
chrX 155270560 12550567 0.08083030678835705 0.3758756577731902
chrY 59373566 885204 0.014909059024684486 0.6612101388918408