BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1819153.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 24,975,509
number of mapped reads = 24,407,764 (97.73%)
number of supplementary alignments = 19,969 (0.08%)
number of secondary alignments = 0
number of mapped bases = 1,657,899,146 bp
number of sequenced bases = 1,657,616,039 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,405,763
duplication rate = 1.72%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 48.7419
>>>>>>> ACTG content
number of A's = 465,368,576 bp (28.07%)
number of C's = 357,354,868 bp (21.56%)
number of T's = 484,062,111 bp (29.2%)
number of G's = 350,747,420 bp (21.16%)
number of N's = 83,064 bp (0.01%)
GC percentage = 42.72%
>>>>>>> Mismatches and indels
general error rate = 0.0032
number of mismatches = 5,031,691
number of insertions = 139,166
mapped reads with insertion percentage = 0.57%
number of deletions = 133,420
mapped reads with deletion percentage = 0.54%
homopolymer indels = 35.62%
>>>>>>> Coverage
mean coverageData = 0.5356X
std coverageData = 5.6579X
There is a 36.72% of reference with a coverageData >= 1X
There is a 10.5% of reference with a coverageData >= 2X
There is a 2.65% of reference with a coverageData >= 3X
There is a 0.69% of reference with a coverageData >= 4X
There is a 0.21% of reference with a coverageData >= 5X
There is a 0.09% of reference with a coverageData >= 6X
There is a 0.06% of reference with a coverageData >= 7X
There is a 0.04% of reference with a coverageData >= 8X
There is a 0.04% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.03% of reference with a coverageData >= 11X
There is a 0.03% of reference with a coverageData >= 12X
There is a 0.02% of reference with a coverageData >= 13X
There is a 0.02% of reference with a coverageData >= 14X
There is a 0.02% of reference with a coverageData >= 15X
There is a 0.02% of reference with a coverageData >= 16X
There is a 0.02% of reference with a coverageData >= 17X
There is a 0.02% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.02% of reference with a coverageData >= 20X
There is a 0.02% of reference with a coverageData >= 21X
There is a 0.02% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 160793908 0.6451093576212193 10.186097986708536
chr2 243199373 129118037 0.5309143498490845 4.059977113468862
chr3 198022430 89461133 0.45177272594826756 2.782446676531036
chr4 191154276 93569527 0.48949743086050557 3.85146711275238
chr5 180915260 88905360 0.4914199056508555 0.9461166661840776
chr6 171115067 70925973 0.4144928570200075 2.099194300965606
chr7 159138663 80502018 0.5058608416233835 3.5295469150862164
chr8 146364022 139815356 0.9552576793769715 2.054370813948859
chr9 141213431 68226600 0.48314526116145423 3.2727651247911176
chr10 135534747 97769879 0.7213639392413519 17.042414880411147
chr11 135006516 58561532 0.43376818938131845 1.925686567575435
chr12 133851895 73989834 0.5527738998390721 0.9813225288698424
chr13 115169878 37436653 0.3250559404083071 0.7046921547703178
chr14 107349540 39003627 0.36333296817107924 0.865638902395483
chr15 102531392 43043951 0.4198124121829927 0.7305880415671293
chr16 90354753 59387334 0.6572685113753783 5.421858872433642
chr17 81195210 59387061 0.7314108923420483 1.907415553332596
chr18 78077248 38786021 0.496764704104325 5.145392172077098
chr19 59128983 34959394 0.591239561823683 7.066905962885582
chr20 63025520 47622730 0.7556102670791134 1.5462676144993557
chr21 48129895 23430283 0.4868135074884331 3.5768849414019184
chr22 51304566 15634613 0.3047411608549617 0.8955150771387055
chrMT 16571 11060470 667.4594170538893 202.38381657059185
chrX 155270560 88122477 0.5675414386346002 1.3642889391254993
chrY 59373566 8385375 0.14123077936737033 6.4342467185247045