BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR975271.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 = 48,819,372
number of mapped reads = 48,572,589 (99.49%)
number of supplementary alignments = 82,914 (0.17%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 24,354,460
number of mapped paired reads (second in pair) = 24,218,129
number of mapped paired reads (both in pair) = 48,380,282
number of mapped paired reads (singletons) = 192,307
number of mapped bases = 4,550,326,316 bp
number of sequenced bases = 4,548,690,138 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 32,473,311
duplication rate = 60.05%
>>>>>>> Insert size
mean insert size = 85,006.8216
std insert size = 2,909,308.7229
median insert size = 230
>>>>>>> Mapping quality
mean mapping quality = 56.2248
>>>>>>> ACTG content
number of A's = 1,234,405,226 bp (27.14%)
number of C's = 1,003,373,800 bp (22.06%)
number of T's = 1,245,668,267 bp (27.39%)
number of G's = 1,064,254,148 bp (23.4%)
number of N's = 988,697 bp (0.02%)
GC percentage = 45.46%
>>>>>>> Mismatches and indels
general error rate = 0.0086
number of mismatches = 38,488,395
number of insertions = 474,487
mapped reads with insertion percentage = 0.97%
number of deletions = 1,163,006
mapped reads with deletion percentage = 2.36%
homopolymer indels = 47.52%
>>>>>>> Coverage
mean coverageData = 1.4699X
std coverageData = 23.5445X
There is a 7.12% of reference with a coverageData >= 1X
There is a 4.55% of reference with a coverageData >= 2X
There is a 2.8% of reference with a coverageData >= 3X
There is a 2.27% of reference with a coverageData >= 4X
There is a 1.93% of reference with a coverageData >= 5X
There is a 1.76% of reference with a coverageData >= 6X
There is a 1.63% of reference with a coverageData >= 7X
There is a 1.54% of reference with a coverageData >= 8X
There is a 1.47% of reference with a coverageData >= 9X
There is a 1.41% of reference with a coverageData >= 10X
There is a 1.35% of reference with a coverageData >= 11X
There is a 1.3% of reference with a coverageData >= 12X
There is a 1.26% of reference with a coverageData >= 13X
There is a 1.22% of reference with a coverageData >= 14X
There is a 1.19% of reference with a coverageData >= 15X
There is a 1.15% of reference with a coverageData >= 16X
There is a 1.12% of reference with a coverageData >= 17X
There is a 1.09% of reference with a coverageData >= 18X
There is a 1.06% of reference with a coverageData >= 19X
There is a 1.04% of reference with a coverageData >= 20X
There is a 1.01% of reference with a coverageData >= 21X
There is a 0.99% of reference with a coverageData >= 22X
There is a 0.97% of reference with a coverageData >= 23X
There is a 0.95% of reference with a coverageData >= 24X
There is a 0.93% of reference with a coverageData >= 25X
There is a 0.91% of reference with a coverageData >= 26X
There is a 0.89% of reference with a coverageData >= 27X
There is a 0.87% of reference with a coverageData >= 28X
There is a 0.86% of reference with a coverageData >= 29X
There is a 0.84% of reference with a coverageData >= 30X
There is a 0.83% of reference with a coverageData >= 31X
There is a 0.81% of reference with a coverageData >= 32X
There is a 0.8% of reference with a coverageData >= 33X
There is a 0.78% of reference with a coverageData >= 34X
There is a 0.77% of reference with a coverageData >= 35X
There is a 0.76% of reference with a coverageData >= 36X
There is a 0.74% of reference with a coverageData >= 37X
There is a 0.73% of reference with a coverageData >= 38X
There is a 0.72% of reference with a coverageData >= 39X
There is a 0.71% of reference with a coverageData >= 40X
There is a 0.7% of reference with a coverageData >= 41X
There is a 0.69% of reference with a coverageData >= 42X
There is a 0.68% of reference with a coverageData >= 43X
There is a 0.67% of reference with a coverageData >= 44X
There is a 0.66% of reference with a coverageData >= 45X
There is a 0.65% of reference with a coverageData >= 46X
There is a 0.64% of reference with a coverageData >= 47X
There is a 0.63% of reference with a coverageData >= 48X
There is a 0.62% of reference with a coverageData >= 49X
There is a 0.61% of reference with a coverageData >= 50X
There is a 0.6% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 545430673 2.1882821026151023 29.944554144083718
chr2 243199373 392248731 1.6128690060397484 23.7195461723444
chr3 198022430 309194882 1.56141343180164 23.16316931916195
chr4 191154276 133302029 0.6973531107407716 13.60451665487559
chr5 180915260 219447997 1.2129877656533783 19.53985394169701
chr6 171115067 412113479 2.4083997173667937 39.14028848884581
chr7 159138663 251050823 1.5775602123790622 26.756919070721388
chr8 146364022 150064239 1.0252809191045598 16.007497736597752
chr9 141213431 183959304 1.3027040182884586 19.889156634308318
chr10 135534747 201348024 1.4855823208199148 22.450840510155917
chr11 135006516 211787586 1.568721216389289 23.044446989709638
chr12 133851895 245994523 1.8378112838820848 23.76056926572627
chr13 115169878 98491551 0.8551849902975498 19.723617138132408
chr14 107349540 148635689 1.3845954905815152 20.817488117868553
chr15 102531392 167862527 1.637181781361166 23.646973349241392
chr16 90354753 131880895 1.4595900118281548 21.439993045576905
chr17 81195210 157998174 1.9459051094270217 26.551963735228732
chr18 78077248 82840403 1.0610056722286114 18.15245744455452
chr19 59128983 174058379 2.943706625226414 35.323651188386854
chr20 63025520 108112915 1.715383149555926 25.620174301754222
chr21 48129895 40649194 0.8445726715173594 20.447406242721456
chr22 51304566 72263351 1.4085169534423116 21.447710724665125
chrMT 16571 61848 3.7323034216402147 12.07232165704945
chrX 155270560 103623460 0.6673735188434948 12.81132804701786
chrY 59373566 7905640 0.1331508368555798 5.221069657866994