BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6063537.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 = 4,706,434
number of mapped reads = 4,409,319 (93.69%)
number of supplementary alignments = 44,614 (0.95%)
number of secondary alignments = 0
number of mapped bases = 288,816,557 bp
number of sequenced bases = 288,713,923 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,331,400
duplication rate = 17.48%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7306
>>>>>>> ACTG content
number of A's = 75,413,004 bp (26.12%)
number of C's = 52,624,883 bp (18.23%)
number of T's = 93,122,026 bp (32.25%)
number of G's = 67,520,755 bp (23.39%)
number of N's = 33,255 bp (0.01%)
GC percentage = 41.61%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 1,413,444
number of insertions = 19,282
mapped reads with insertion percentage = 0.43%
number of deletions = 58,164
mapped reads with deletion percentage = 1.3%
homopolymer indels = 45.75%
>>>>>>> Coverage
mean coverageData = 0.0933X
std coverageData = 1.0422X
There is a 3.5% of reference with a coverageData >= 1X
There is a 1.98% of reference with a coverageData >= 2X
There is a 1.27% of reference with a coverageData >= 3X
There is a 0.82% of reference with a coverageData >= 4X
There is a 0.54% of reference with a coverageData >= 5X
There is a 0.36% of reference with a coverageData >= 6X
There is a 0.23% of reference with a coverageData >= 7X
There is a 0.15% of reference with a coverageData >= 8X
There is a 0.1% of reference with a coverageData >= 9X
There is a 0.07% of reference with a coverageData >= 10X
There is a 0.04% 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 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% 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 32094967 0.1287658456826874 1.6151153662609397
chr2 243199373 28593514 0.11757231791876371 1.6615976842026423
chr3 198022430 19995964 0.10097827806678264 0.6844062216542678
chr4 191154276 13277859 0.06946148042223235 0.5927455426535974
chr5 180915260 13570455 0.07501000744768573 0.586686923003838
chr6 171115067 19865838 0.1160963692343936 0.8494803600549822
chr7 159138663 20066978 0.12609743994141764 1.3213753153947796
chr8 146364022 11242212 0.07680994172188026 1.7540482843529985
chr9 141213431 8958121 0.06343674915738008 0.6985839291901731
chr10 135534747 14695508 0.10842612927886308 0.8338258686583504
chr11 135006516 14212957 0.1052760816374226 0.7661224361757498
chr12 133851895 11593150 0.0866117734082136 0.6389720199774239
chr13 115169878 5830053 0.05062133520711032 0.5330721897321115
chr14 107349540 6526320 0.060795043928460246 0.5566940107879631
chr15 102531392 5099366 0.04973468028211302 0.4840187082078498
chr16 90354753 5689457 0.06296798797070476 0.5577751378504818
chr17 81195210 8593862 0.10584198255044848 0.7249736235402067
chr18 78077248 7327342 0.09384733949639208 1.223191123741751
chr19 59128983 7268652 0.12292875052493292 1.1594400908194173
chr20 63025520 4149322 0.0658355853311484 0.5675497467104321
chr21 48129895 5100484 0.10597330411794997 0.7098647450491976
chr22 51304566 3421286 0.06668579946665956 0.5457965143775033
chrMT 16571 1215219 73.33407760545532 55.116593090840446
chrX 155270560 19764891 0.1272932293153319 0.8288138609820909
chrY 59373566 662780 0.011162880127496468 0.27902706980075637