BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR975288.sorted.bam
outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 5,650,368
number of mapped reads = 5,590,106 (98.93%)
number of supplementary alignments = 37,980 (0.67%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 2,793,390
number of mapped paired reads (second in pair) = 2,796,716
number of mapped paired reads (both in pair) = 5,563,968
number of mapped paired reads (singletons) = 26,138
number of mapped bases = 519,311,714 bp
number of sequenced bases = 518,989,721 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 406,925
duplication rate = 3.07%
>>>>>>> Insert size
mean insert size = 78,447.2576
std insert size = 2,630,319.741
median insert size = 174
>>>>>>> Mapping quality
mean mapping quality = 52.4473
>>>>>>> ACTG content
number of A's = 155,737,059 bp (30.01%)
number of C's = 101,102,379 bp (19.48%)
number of T's = 154,653,463 bp (29.8%)
number of G's = 107,482,834 bp (20.71%)
number of N's = 13,986 bp (0%)
GC percentage = 40.19%
>>>>>>> Mismatches and indels
general error rate = 0.0088
number of mismatches = 4,359,630
number of insertions = 95,302
mapped reads with insertion percentage = 1.66%
number of deletions = 173,211
mapped reads with deletion percentage = 3.03%
homopolymer indels = 45.42%
>>>>>>> Coverage
mean coverageData = 0.1678X
std coverageData = 2.4016X
There is a 10.98% of reference with a coverageData >= 1X
There is a 3.28% of reference with a coverageData >= 2X
There is a 0.84% of reference with a coverageData >= 3X
There is a 0.27% of reference with a coverageData >= 4X
There is a 0.1% of reference with a coverageData >= 5X
There is a 0.05% of reference with a coverageData >= 6X
There is a 0.03% of reference with a coverageData >= 7X
There is a 0.02% of reference with a coverageData >= 8X
There is a 0.02% of reference with a coverageData >= 9X
There is a 0.02% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.01% 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 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% 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 46641164 0.1871255678837406 2.507214847780491
chr2 243199373 45170320 0.18573370252891236 2.4900388719070716
chr3 198022430 25993324 0.1312645441226027 0.5782455137554654
chr4 191154276 36271691 0.18975087431473414 1.9191887662431066
chr5 180915260 31911556 0.1763895207070979 0.5689359313193825
chr6 171115067 44301300 0.2588977158861177 1.3691142145298965
chr7 159138663 29158603 0.18322764845649106 2.523192897183401
chr8 146364022 25928070 0.1771478376017844 0.8933452786631315
chr9 141213431 22717824 0.16087580224575096 3.6137022329922095
chr10 135534747 29337597 0.21645812346556415 6.766855314031
chr11 135006516 16477385 0.12204881281433853 1.789731699938576
chr12 133851895 22650423 0.16922003980593625 0.5488806829441817
chr13 115169878 16415436 0.14253237291785617 0.4930534632208118
chr14 107349540 15046489 0.14016351630384258 0.6234601622584712
chr15 102531392 13960916 0.13616235698818954 0.4778647980870633
chr16 90354753 17347164 0.19198950164802067 3.8859405331485557
chr17 81195210 9941894 0.12244434123638574 1.5758379646617755
chr18 78077248 15292237 0.19586034845900308 3.461027813343567
chr19 59128983 6328860 0.10703481911738613 1.4395309625704937
chr20 63025520 9877447 0.15672138841535938 0.7055580394054433
chr21 48129895 6426223 0.1335183257723708 0.9268682185370656
chr22 51304566 4503655 0.08778273263241326 0.43198917946319176
chrMT 16571 112139 6.767183634059502 4.8613348686436115
chrX 155270560 17147022 0.11043318192450649 0.877454084184839
chrY 59373566 10352975 0.17437010605022443 4.213407370818615