BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716179.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 = 572,043
number of mapped reads = 524,778 (91.74%)
number of supplementary alignments = 1,864 (0.33%)
number of secondary alignments = 0
number of mapped bases = 30,392,153 bp
number of sequenced bases = 30,382,584 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 13,458
duplication rate = 1.9%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6363
>>>>>>> ACTG content
number of A's = 7,413,651 bp (24.4%)
number of C's = 5,953,620 bp (19.6%)
number of T's = 9,511,824 bp (31.31%)
number of G's = 7,502,874 bp (24.69%)
number of N's = 615 bp (0%)
GC percentage = 44.29%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 152,492
number of insertions = 1,904
mapped reads with insertion percentage = 0.36%
number of deletions = 5,845
mapped reads with deletion percentage = 1.1%
homopolymer indels = 43.64%
>>>>>>> Coverage
mean coverageData = 0.0098X
std coverageData = 0.1264X
There is a 0.92% of reference with a coverageData >= 1X
There is a 0.04% of reference with a coverageData >= 2X
There is a 0% 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 2510844 0.010073571692324892 0.17862108461036033
chr2 243199373 2551850 0.010492831328146558 0.16722678754190057
chr3 198022430 1998297 0.010091265923764293 0.10535202562208489
chr4 191154276 1914427 0.010015088545547368 0.11553059777090756
chr5 180915260 1807347 0.009990019636817811 0.10420839779326613
chr6 171115067 1671344 0.009767368995040045 0.10826321008456828
chr7 159138663 1655576 0.01040335496597706 0.13621882278147707
chr8 146364022 1540040 0.010521984699217954 0.14224210709388024
chr9 141213431 1309414 0.009272588242686348 0.10944320997990493
chr10 135534747 1480598 0.010924121177575224 0.14086132542443944
chr11 135006516 1374840 0.010183508475990892 0.11488089952784782
chr12 133851895 1338810 0.010002174418225457 0.10476028290613676
chr13 115169878 919546 0.007984257828249153 0.09317335641962143
chr14 107349540 927031 0.008635630855986901 0.09863499760490921
chr15 102531392 875294 0.008536839137032296 0.09623937291215492
chr16 90354753 917384 0.01015313494354857 0.10851394093546322
chr17 81195210 878132 0.01081507148020185 0.11099145900496767
chr18 78077248 777416 0.009957010779888144 0.15053641143587457
chr19 59128983 675387 0.01142226647124981 0.15103624720450415
chr20 63025520 685324 0.01087375399679368 0.10922951487902306
chr21 48129895 401976 0.008351898544553234 0.10508000590335628
chr22 51304566 379007 0.007387393161068744 0.08965423736184697
chrMT 16571 5777 0.34862108502806105 0.6255775675079924
chrX 155270560 1675022 0.010787762986106316 0.11281348331987377
chrY 59373566 121470 0.002045859937063575 0.10061229296156898