BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1006165.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 3,995,916
number of mapped reads = 3,383,122 (84.66%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 1,700,774
number of mapped paired reads (second in pair) = 1,682,348
number of mapped paired reads (both in pair) = 3,122,498
number of mapped paired reads (singletons) = 260,624
number of mapped bases = 130,997,141 bp
number of sequenced bases = 130,979,737 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 96,825
duplication rate = 2.42%
>>>>>>> Insert size
mean insert size = 80,401.2485
std insert size = 2,677,874.6192
median insert size = 175
>>>>>>> Mapping quality
mean mapping quality = 48.2406
>>>>>>> ACTG content
number of A's = 36,736,206 bp (28.05%)
number of C's = 28,208,103 bp (21.54%)
number of T's = 37,486,853 bp (28.62%)
number of G's = 28,543,669 bp (21.79%)
number of N's = 4,906 bp (0%)
GC percentage = 43.33%
>>>>>>> Mismatches and indels
general error rate = 0.003
number of mismatches = 387,055
number of insertions = 3,750
mapped reads with insertion percentage = 0.11%
number of deletions = 12,996
mapped reads with deletion percentage = 0.38%
homopolymer indels = 44.64%
>>>>>>> Coverage
mean coverageData = 0.0423X
std coverageData = 0.2882X
There is a 3.77% of reference with a coverageData >= 1X
There is a 0.37% of reference with a coverageData >= 2X
There is a 0.04% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% 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 10605200 0.042548339327908836 0.3904475425139352
chr2 243199373 11309575 0.046503306568968825 0.2657139334201031
chr3 198022430 8991427 0.04540610374289417 0.23117443963373682
chr4 191154276 8405812 0.04397396791688824 0.24686354381267972
chr5 180915260 7789009 0.04305335547703383 0.2255585630102546
chr6 171115067 7419173 0.043357800865075194 0.24377004037591005
chr7 159138663 7006604 0.04402829499704921 0.2934337042579644
chr8 146364022 6412501 0.04381200319843629 0.5479751055724652
chr9 141213431 5593789 0.03961230146727332 0.23452281400466737
chr10 135534747 6313735 0.04658388450011273 0.3306249489548835
chr11 135006516 6090567 0.04511313365052691 0.25402752946392815
chr12 133851895 5697268 0.04256396967708227 0.2249199795674939
chr13 115169878 4126295 0.03582790111143471 0.20426135249347782
chr14 107349540 4088216 0.0380832186146303 0.2974338094137083
chr15 102531392 3703173 0.0361174556178853 0.20606022473771085
chr16 90354753 4047445 0.04479504249211992 0.29512282752835967
chr17 81195210 3628052 0.044683079211199773 0.23549555482512047
chr18 78077248 3331989 0.042675543584732904 0.3343854170547275
chr19 59128983 2608408 0.04411386544564786 0.31062824875822287
chr20 63025520 2859600 0.045372096890275555 0.23616537951249225
chr21 48129895 1731995 0.03598584621886252 0.2205632558138533
chr22 51304566 1709942 0.03332923623211236 0.2008030609442233
chrMT 16571 2562 0.15460744674431234 0.42120314418990445
chrX 155270560 7163312 0.04613438632539227 0.24306333211607695
chrY 59373566 361492 0.00608843336106846 0.17805481172998944