BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238335.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,207,495
number of mapped reads = 2,926,952 (91.25%)
number of supplementary alignments = 27,570 (0.86%)
number of secondary alignments = 0
number of mapped bases = 195,119,832 bp
number of sequenced bases = 195,028,285 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 123,088
duplication rate = 2.95%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.7651
>>>>>>> ACTG content
number of A's = 54,699,381 bp (28.05%)
number of C's = 37,454,081 bp (19.2%)
number of T's = 59,592,853 bp (30.56%)
number of G's = 43,219,785 bp (22.16%)
number of N's = 62,185 bp (0.03%)
GC percentage = 41.37%
>>>>>>> Mismatches and indels
general error rate = 0.0085
number of mismatches = 1,627,752
number of insertions = 14,363
mapped reads with insertion percentage = 0.49%
number of deletions = 53,041
mapped reads with deletion percentage = 1.79%
homopolymer indels = 45.68%
>>>>>>> Coverage
mean coverageData = 0.063X
std coverageData = 0.5737X
There is a 5.26% of reference with a coverageData >= 1X
There is a 0.74% of reference with a coverageData >= 2X
There is a 0.13% of reference with a coverageData >= 3X
There is a 0.03% 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% 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 19053771 0.0764442267929194 1.1484284356910872
chr2 243199373 16039521 0.06595214782893376 0.6735603576008451
chr3 198022430 11855770 0.05987084392409486 0.2804024732361228
chr4 191154276 11352570 0.05938956866442266 0.3013896156068685
chr5 180915260 14542884 0.08038505983409028 0.33080258756275827
chr6 171115067 13879681 0.0811131435900966 0.4553434143453786
chr7 159138663 9589082 0.060256142782850956 0.7417537290015008
chr8 146364022 8468599 0.05785984071959979 0.784172916882382
chr9 141213431 6915585 0.04897257258765988 0.5140378369038664
chr10 135534747 8325228 0.06142504549036418 0.49943354523542
chr11 135006516 7939248 0.05880640605524551 0.43895934759354044
chr12 133851895 10049438 0.07507878764062324 0.3295352351038755
chr13 115169878 4282117 0.03718087640936808 0.2225261323567521
chr14 107349540 5576687 0.051948867223837195 0.30587724868830235
chr15 102531392 5222842 0.05093895535915478 0.26796588215365
chr16 90354753 5284993 0.05849158815142796 0.331904092972799
chr17 81195210 4208923 0.051837084970899144 0.30765223532556896
chr18 78077248 6149410 0.0787605884879549 0.9951668989381797
chr19 59128983 3474622 0.0587634324777749 0.8485749562869999
chr20 63025520 4499854 0.07139733238218424 0.3174675433403494
chr21 48129895 2202719 0.045766129346428035 0.2774708682569631
chr22 51304566 2459377 0.04793680546873742 0.25177061761055974
chrMT 16571 12437 0.7505280308973508 0.9931782584388458
chrX 155270560 13207426 0.08506072239322122 0.40653776503082717
chrY 59373566 527048 0.008876812283769514 0.18738074459213405