BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1777265.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 51,917,058
number of mapped reads = 51,639,720 (99.47%)
number of supplementary alignments = 1,964,095 (3.78%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 25,820,651
number of mapped paired reads (second in pair) = 25,819,069
number of mapped paired reads (both in pair) = 51,543,106
number of mapped paired reads (singletons) = 96,614
number of mapped bases = 5,177,058,900 bp
number of sequenced bases = 5,176,266,796 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 26,560,164
duplication rate = 46.38%
>>>>>>> Insert size
mean insert size = 322,681.1492
std insert size = 5,599,118.6054
median insert size = 229
>>>>>>> Mapping quality
mean mapping quality = 54.6178
>>>>>>> ACTG content
number of A's = 1,431,228,259 bp (27.65%)
number of C's = 1,159,907,996 bp (22.41%)
number of T's = 1,420,949,875 bp (27.45%)
number of G's = 1,164,117,509 bp (22.49%)
number of N's = 63,157 bp (0%)
GC percentage = 44.9%
>>>>>>> Mismatches and indels
general error rate = 0.0022
number of mismatches = 10,103,784
number of insertions = 822,212
mapped reads with insertion percentage = 1.57%
number of deletions = 358,431
mapped reads with deletion percentage = 0.69%
homopolymer indels = 51.72%
>>>>>>> Coverage
mean coverageData = 1.6723X
std coverageData = 14.7407X
There is a 17.16% of reference with a coverageData >= 1X
There is a 9.78% of reference with a coverageData >= 2X
There is a 6.17% of reference with a coverageData >= 3X
There is a 4.62% of reference with a coverageData >= 4X
There is a 3.75% of reference with a coverageData >= 5X
There is a 3.28% of reference with a coverageData >= 6X
There is a 2.94% of reference with a coverageData >= 7X
There is a 2.72% of reference with a coverageData >= 8X
There is a 2.54% of reference with a coverageData >= 9X
There is a 2.4% of reference with a coverageData >= 10X
There is a 2.27% of reference with a coverageData >= 11X
There is a 2.17% of reference with a coverageData >= 12X
There is a 2.08% of reference with a coverageData >= 13X
There is a 1.99% of reference with a coverageData >= 14X
There is a 1.92% of reference with a coverageData >= 15X
There is a 1.85% of reference with a coverageData >= 16X
There is a 1.79% of reference with a coverageData >= 17X
There is a 1.73% of reference with a coverageData >= 18X
There is a 1.67% of reference with a coverageData >= 19X
There is a 1.62% of reference with a coverageData >= 20X
There is a 1.57% of reference with a coverageData >= 21X
There is a 1.53% of reference with a coverageData >= 22X
There is a 1.48% of reference with a coverageData >= 23X
There is a 1.44% of reference with a coverageData >= 24X
There is a 1.4% of reference with a coverageData >= 25X
There is a 1.36% of reference with a coverageData >= 26X
There is a 1.33% of reference with a coverageData >= 27X
There is a 1.29% of reference with a coverageData >= 28X
There is a 1.26% of reference with a coverageData >= 29X
There is a 1.23% of reference with a coverageData >= 30X
There is a 1.2% of reference with a coverageData >= 31X
There is a 1.17% of reference with a coverageData >= 32X
There is a 1.14% of reference with a coverageData >= 33X
There is a 1.12% of reference with a coverageData >= 34X
There is a 1.09% of reference with a coverageData >= 35X
There is a 1.07% of reference with a coverageData >= 36X
There is a 1.04% of reference with a coverageData >= 37X
There is a 1.02% of reference with a coverageData >= 38X
There is a 1% of reference with a coverageData >= 39X
There is a 0.97% of reference with a coverageData >= 40X
There is a 0.95% of reference with a coverageData >= 41X
There is a 0.93% of reference with a coverageData >= 42X
There is a 0.91% of reference with a coverageData >= 43X
There is a 0.9% of reference with a coverageData >= 44X
There is a 0.88% of reference with a coverageData >= 45X
There is a 0.86% of reference with a coverageData >= 46X
There is a 0.84% of reference with a coverageData >= 47X
There is a 0.83% of reference with a coverageData >= 48X
There is a 0.81% of reference with a coverageData >= 49X
There is a 0.79% of reference with a coverageData >= 50X
There is a 0.78% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 529751029 2.1253749614529545 16.651274772515556
chr2 243199373 472822939 1.944178281249105 16.47861692527107
chr3 198022430 318038389 1.6060725494581598 14.324545870655978
chr4 191154276 234382016 1.226140586046843 12.273344300948404
chr5 180915260 271100179 1.4984926036642792 12.981332015245446
chr6 171115067 245377303 1.433990047176851 12.986655446395837
chr7 159138663 326861343 2.0539404871084033 17.02433385551543
chr8 146364022 175911989 1.201879987965895 13.135740347852904
chr9 141213431 178812049 1.2662538381352693 11.499400468215887
chr10 135534747 223995306 1.6526780840930777 14.030623752987756
chr11 135006516 338195397 2.5050301794322283 19.42338041928218
chr12 133851895 296470899 2.214917457836514 17.134556439386078
chr13 115169878 151223108 1.3130439193484256 13.965195635482688
chr14 107349540 118832694 1.1069697550636919 11.070481730859505
chr15 102531392 256096975 2.4977421061444285 19.936473428366288
chr16 90354753 160175512 1.7727403006679683 13.714311891292118
chr17 81195210 225731075 2.7801033459978735 19.15077111142457
chr18 78077248 81144000 1.0392784335841345 10.53073258858827
chr19 59128983 165276601 2.795187615521816 16.980780502524638
chr20 63025520 143334192 2.2742246632792558 17.688502848907362
chr21 48129895 34565610 0.7181733930647469 7.961444276895723
chr22 51304566 55621596 1.0841451421692174 9.22632437653904
chrMT 16571 1193605 72.02975076941645 27.99435566522136
chrX 155270560 170519223 1.0982070458173139 12.593745231861819
chrY 59373566 1625871 0.027383751887161367 1.3339833782908523