BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472643.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,342,350
number of mapped reads = 17,208,560 (99.23%)
number of supplementary alignments = 95,288 (0.55%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 8,625,224
number of mapped paired reads (second in pair) = 8,583,336
number of mapped paired reads (both in pair) = 17,122,564
number of mapped paired reads (singletons) = 85,996
number of mapped bases = 1,692,679,278 bp
number of sequenced bases = 1,692,450,548 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 12,179,479
duplication rate = 48.51%
>>>>>>> Insert size
mean insert size = 19,886.0069
std insert size = 1,349,900.0281
median insert size = 209
>>>>>>> Mapping quality
mean mapping quality = 54.9254
>>>>>>> ACTG content
number of A's = 454,144,596 bp (26.83%)
number of C's = 394,409,085 bp (23.3%)
number of T's = 454,420,212 bp (26.85%)
number of G's = 389,149,910 bp (22.99%)
number of N's = 326,745 bp (0.02%)
GC percentage = 46.3%
>>>>>>> Mismatches and indels
general error rate = 0.0062
number of mismatches = 10,329,719
number of insertions = 113,925
mapped reads with insertion percentage = 0.65%
number of deletions = 93,141
mapped reads with deletion percentage = 0.53%
homopolymer indels = 46.93%
>>>>>>> Coverage
mean coverageData = 0.5468X
std coverageData = 26.5198X
There is a 3.62% of reference with a coverageData >= 1X
There is a 1.69% of reference with a coverageData >= 2X
There is a 0.79% of reference with a coverageData >= 3X
There is a 0.58% of reference with a coverageData >= 4X
There is a 0.43% of reference with a coverageData >= 5X
There is a 0.38% of reference with a coverageData >= 6X
There is a 0.34% of reference with a coverageData >= 7X
There is a 0.31% of reference with a coverageData >= 8X
There is a 0.3% of reference with a coverageData >= 9X
There is a 0.28% of reference with a coverageData >= 10X
There is a 0.27% of reference with a coverageData >= 11X
There is a 0.26% of reference with a coverageData >= 12X
There is a 0.25% of reference with a coverageData >= 13X
There is a 0.24% of reference with a coverageData >= 14X
There is a 0.24% of reference with a coverageData >= 15X
There is a 0.23% of reference with a coverageData >= 16X
There is a 0.22% of reference with a coverageData >= 17X
There is a 0.22% of reference with a coverageData >= 18X
There is a 0.21% of reference with a coverageData >= 19X
There is a 0.21% of reference with a coverageData >= 20X
There is a 0.2% of reference with a coverageData >= 21X
There is a 0.2% of reference with a coverageData >= 22X
There is a 0.2% of reference with a coverageData >= 23X
There is a 0.19% of reference with a coverageData >= 24X
There is a 0.19% of reference with a coverageData >= 25X
There is a 0.19% of reference with a coverageData >= 26X
There is a 0.18% of reference with a coverageData >= 27X
There is a 0.18% of reference with a coverageData >= 28X
There is a 0.18% of reference with a coverageData >= 29X
There is a 0.17% of reference with a coverageData >= 30X
There is a 0.17% of reference with a coverageData >= 31X
There is a 0.17% of reference with a coverageData >= 32X
There is a 0.17% of reference with a coverageData >= 33X
There is a 0.16% of reference with a coverageData >= 34X
There is a 0.16% of reference with a coverageData >= 35X
There is a 0.16% of reference with a coverageData >= 36X
There is a 0.16% of reference with a coverageData >= 37X
There is a 0.15% of reference with a coverageData >= 38X
There is a 0.15% of reference with a coverageData >= 39X
There is a 0.15% of reference with a coverageData >= 40X
There is a 0.15% of reference with a coverageData >= 41X
There is a 0.15% of reference with a coverageData >= 42X
There is a 0.15% of reference with a coverageData >= 43X
There is a 0.14% of reference with a coverageData >= 44X
There is a 0.14% of reference with a coverageData >= 45X
There is a 0.14% of reference with a coverageData >= 46X
There is a 0.14% of reference with a coverageData >= 47X
There is a 0.14% of reference with a coverageData >= 48X
There is a 0.14% of reference with a coverageData >= 49X
There is a 0.13% of reference with a coverageData >= 50X
There is a 0.13% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 208169250 0.835180466812157 36.118444901200995
chr2 243199373 73298178 0.3013913115639488 13.45891397316359
chr3 198022430 138527857 0.6995563936873211 32.66092474775991
chr4 191154276 75642631 0.3957150872209628 23.13671248748448
chr5 180915260 80336667 0.44405688608025656 20.736026334643345
chr6 171115067 116388928 0.6801793088156287 29.989083275796233
chr7 159138663 83291626 0.523390258720472 20.457118417259146
chr8 146364022 102265315 0.6987052801814916 31.546225911620873
chr9 141213431 78999027 0.5594299808493428 21.519208271161283
chr10 135534747 48447406 0.3574537679256523 19.173664101535888
chr11 135006516 77481684 0.5739106992435832 40.50064173465941
chr12 133851895 84344894 0.6301359722998319 23.840980289417267
chr13 115169878 30780832 0.267264605420525 12.2803353890003
chr14 107349540 59265227 0.5520771397809436 26.12160728070737
chr15 102531392 44895369 0.4378694965928093 19.844675222347615
chr16 90354753 87924847 0.9731070483917985 34.40715084756745
chr17 81195210 87376049 1.076123197415217 37.253439471043556
chr18 78077248 24243247 0.31050334919591427 13.968567376375443
chr19 59128983 68592937 1.1600560929654413 51.38351241760845
chr20 63025520 32785467 0.520193518435072 20.08086568729704
chr21 48129895 6719773 0.13961744566448775 7.478854304654106
chr22 51304566 31236415 0.6088427879888897 24.33847758726758
chrMT 16571 2224 0.13421036750950455 0.42672731427909244
chrX 155270560 49656667 0.3198073543368427 19.150096505392924
chrY 59373566 2006761 0.03379889629671225 1.5254271276658655