BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525256.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 = 1,366,965
number of mapped reads = 1,255,186 (91.82%)
number of supplementary alignments = 5,127 (0.38%)
number of secondary alignments = 0
number of mapped bases = 73,031,682 bp
number of sequenced bases = 73,008,618 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 38,149
duplication rate = 2.22%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.8561
>>>>>>> ACTG content
number of A's = 17,656,424 bp (24.18%)
number of C's = 13,286,781 bp (18.2%)
number of T's = 23,875,372 bp (32.7%)
number of G's = 18,188,684 bp (24.91%)
number of N's = 1,357 bp (0%)
GC percentage = 43.11%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 362,397
number of insertions = 5,032
mapped reads with insertion percentage = 0.4%
number of deletions = 14,680
mapped reads with deletion percentage = 1.16%
homopolymer indels = 44.88%
>>>>>>> Coverage
mean coverageData = 0.0236X
std coverageData = 0.236X
There is a 2.16% of reference with a coverageData >= 1X
There is a 0.14% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 7765561 0.031155633509936168 0.3670894599171239
chr2 243199373 5815627 0.023913001617812558 0.3016034089099842
chr3 198022430 7436119 0.03755190257992491 0.20815286371557834
chr4 191154276 3260792 0.017058430856132144 0.14550929852264452
chr5 180915260 3113347 0.01720886894781568 0.13989295203472377
chr6 171115067 4452106 0.026018199788333075 0.18865649743791243
chr7 159138663 5415952 0.034032911285675434 0.44887860406169794
chr8 146364022 4060033 0.027739282813641183 0.2463641459918828
chr9 141213431 2310425 0.016361226999717895 0.16389364513254692
chr10 135534747 3731378 0.02753078514987747 0.2543135913301352
chr11 135006516 3210055 0.023777037546839592 0.1889621240401237
chr12 133851895 2917794 0.021798675319464098 0.15984963328737317
chr13 115169878 2443616 0.021217492302978737 0.15684255333102778
chr14 107349540 1988040 0.018519315499628597 0.14927498425864544
chr15 102531392 2015995 0.019662222083164538 0.1509830280602796
chr16 90354753 1875625 0.020758454178940646 0.16560447013397653
chr17 81195210 1350630 0.01663435564733437 0.1403057637041021
chr18 78077248 1506411 0.019293853697302445 0.28485521144627035
chr19 59128983 1010838 0.01709547414336553 0.25667982030788183
chr20 63025520 1517317 0.024074644683613877 0.168848622421461
chr21 48129895 937980 0.019488511246492434 0.15303663677599946
chr22 51304566 626537 0.012212109931891832 0.11740633125113067
chrMT 16571 125392 7.566954317784081 5.089242063864677
chrX 155270560 3941314 0.025383524088532946 0.18013882221459165
chrY 59373566 202798 0.0034156277559612975 0.10039950275284715