BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6008665.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 = 2,750,975
number of mapped reads = 2,242,107 (81.5%)
number of supplementary alignments = 23,385 (0.85%)
number of secondary alignments = 0
number of mapped bases = 145,383,015 bp
number of sequenced bases = 145,322,993 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 170,325
duplication rate = 6.21%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.8206
>>>>>>> ACTG content
number of A's = 39,273,256 bp (27.02%)
number of C's = 26,890,306 bp (18.5%)
number of T's = 45,773,738 bp (31.5%)
number of G's = 33,323,057 bp (22.93%)
number of N's = 62,636 bp (0.04%)
GC percentage = 41.43%
>>>>>>> Mismatches and indels
general error rate = 0.0086
number of mismatches = 1,225,430
number of insertions = 10,542
mapped reads with insertion percentage = 0.47%
number of deletions = 37,058
mapped reads with deletion percentage = 1.64%
homopolymer indels = 47.18%
>>>>>>> Coverage
mean coverageData = 0.047X
std coverageData = 0.4039X
There is a 3.44% of reference with a coverageData >= 1X
There is a 0.85% of reference with a coverageData >= 2X
There is a 0.23% 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% 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 11075536 0.04443533964154096 0.6960392101038665
chr2 243199373 15870947 0.06525899637085002 0.5447127904483873
chr3 198022430 9407605 0.047507774750567396 0.2831673879649293
chr4 191154276 9628107 0.05036825333690155 0.30467618951235864
chr5 180915260 8561570 0.047323647546370605 0.2836032717664089
chr6 171115067 6919607 0.040438326801461616 0.3114614744327354
chr7 159138663 8756402 0.05502372481286964 0.5438884055932742
chr8 146364022 7428278 0.050752076217200424 0.4013439862167359
chr9 141213431 6693785 0.04740190046087047 0.385860292851385
chr10 135534747 6290223 0.046410408690252695 0.39181190794249426
chr11 135006516 6146588 0.045528083992627436 0.33496362144788877
chr12 133851895 8055462 0.06018190478364165 0.33058538246638797
chr13 115169878 3414214 0.02964502575925278 0.2221483994245779
chr14 107349540 3923330 0.03654724556807602 0.2693018765047633
chr15 102531392 4058582 0.039583798881809774 0.2666284754554746
chr16 90354753 4367058 0.04833235502287301 0.2964114613303849
chr17 81195210 3772377 0.046460585544393564 0.3153839691831184
chr18 78077248 4527075 0.0579820000827898 0.5794086294433624
chr19 59128983 2511366 0.04247267368018151 0.5062689627330789
chr20 63025520 2581385 0.04095777393030633 0.26945609332348414
chr21 48129895 1716686 0.03566776948090163 0.2561298261066216
chr22 51304566 1618057 0.03153826503473395 0.227229421729125
chrMT 16571 25873 1.561342103675095 1.6211057727715221
chrX 155270560 7701684 0.04960170170056706 0.31434632616457603
chrY 59373566 331218 0.005578543151677971 0.12292939061109968