BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR2094066.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 439,272
number of mapped reads = 424,682 (96.68%)
number of supplementary alignments = 14,876 (3.39%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 213,309
number of mapped paired reads (second in pair) = 211,373
number of mapped paired reads (both in pair) = 421,870
number of mapped paired reads (singletons) = 2,812
number of mapped bases = 56,508,932 bp
number of sequenced bases = 55,375,266 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 409,204
duplication rate = 50.25%
>>>>>>> Insert size
mean insert size = 347,564.5956
std insert size = 5,311,352.5238
median insert size = 168
>>>>>>> Mapping quality
mean mapping quality = 36.7446
>>>>>>> ACTG content
number of A's = 14,578,421 bp (26.33%)
number of C's = 13,152,287 bp (23.75%)
number of T's = 13,901,823 bp (25.1%)
number of G's = 13,742,079 bp (24.82%)
number of N's = 656 bp (0%)
GC percentage = 48.57%
>>>>>>> Mismatches and indels
general error rate = 0.038
number of mismatches = 2,029,648
number of insertions = 31,660
mapped reads with insertion percentage = 7.36%
number of deletions = 165,510
mapped reads with deletion percentage = 37.28%
homopolymer indels = 29.6%
>>>>>>> Coverage
mean coverageData = 0.0183X
std coverageData = 5.4633X
There is a 0.01% of reference with a coverageData >= 1X
There is a 0.01% of reference with a coverageData >= 2X
There is a 0.01% 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 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% 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 535302 0.002147645602054488 0.814216378644869
chr2 243199373 3023524 0.01243228534145933 5.661429932643797
chr3 198022430 1050025 0.005302555877129677 2.6647882636814777
chr4 191154276 762442 0.003988621211905299 1.830137092696487
chr5 180915260 406991 0.0022496222817246043 1.4957941244087136
chr6 171115067 1098198 0.006417891885581297 3.753668345470661
chr7 159138663 1819218 0.011431653161494765 4.831519606433623
chr8 146364022 942327 0.006438242042843015 2.4316673550121677
chr9 141213431 726486 0.005144595629859032 2.454898920697347
chr10 135534747 1016171 0.007497494351024243 2.6489663111281065
chr11 135006516 2014818 0.014923857452924717 4.4515351321658505
chr12 133851895 1816877 0.013573786161189575 5.347657371592676
chr13 115169878 1209573 0.010502511776560187 3.3896920057001645
chr14 107349540 381418 0.003553047362848504 1.5383871570885659
chr15 102531392 974378 0.009503216341781452 3.335667947736544
chr16 90354753 297379 0.0032912380381361897 1.4484289587283263
chr17 81195210 819521 0.010093218553163419 3.588336551331014
chr18 78077248 90940 0.0011647439213021442 0.5109984909166714
chr19 59128983 227340 0.0038448149869244326 1.0819900287130824
chr20 63025520 327606 0.005197989639752278 1.8511011399090969
chr21 48129895 945081 0.019636049486498983 8.493634408966766
chr22 51304566 87981 0.0017148766057196547 0.43325985983442367
chrMT 16571 2133396 128.7427433468107 606.318208159132
chrX 155270560 33186078 0.21373065183766968 18.284888983689893
chrY 59373566 615862 0.010372663147771854 3.3485636742006717