BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3084356.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,083,964
number of mapped reads = 1,868,465 (89.66%)
number of supplementary alignments = 10,309 (0.49%)
number of secondary alignments = 0
number of mapped bases = 123,550,876 bp
number of sequenced bases = 123,508,212 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 57,943
duplication rate = 2.55%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9319
>>>>>>> ACTG content
number of A's = 34,371,679 bp (27.83%)
number of C's = 23,952,449 bp (19.39%)
number of T's = 37,566,650 bp (30.42%)
number of G's = 27,465,141 bp (22.24%)
number of N's = 152,293 bp (0.12%)
GC percentage = 41.63%
>>>>>>> Mismatches and indels
general error rate = 0.0098
number of mismatches = 1,197,423
number of insertions = 8,667
mapped reads with insertion percentage = 0.46%
number of deletions = 24,705
mapped reads with deletion percentage = 1.31%
homopolymer indels = 46.15%
>>>>>>> Coverage
mean coverageData = 0.0399X
std coverageData = 0.2921X
There is a 3.47% of reference with a coverageData >= 1X
There is a 0.4% of reference with a coverageData >= 2X
There is a 0.06% 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 12260185 0.049188182363645944 0.4593280256411451
chr2 243199373 11872022 0.04881600578797545 0.33555079351431466
chr3 198022430 8438643 0.04261458159058042 0.2324781614586611
chr4 191154276 5805726 0.03037193894631999 0.20199254316175896
chr5 180915260 6323338 0.0349519327446452 0.20895297049130288
chr6 171115067 6057105 0.03539784722756179 0.2334164311637169
chr7 159138663 7140221 0.04486792125430889 0.42221490177016896
chr8 146364022 6104137 0.041705173966864614 0.2693072132215274
chr9 141213431 4693156 0.033234487447585635 0.25639157228202875
chr10 135534747 8897996 0.06565103190844485 0.40742222577730314
chr11 135006516 7038171 0.05213208375809061 0.3048123467962199
chr12 133851895 4700308 0.035115737435021 0.2103968691291006
chr13 115169878 3030387 0.026312322741194532 0.1804621076078559
chr14 107349540 3292634 0.030672082991692374 0.20424857269172003
chr15 102531392 2738876 0.026712560383457977 0.1885605022539634
chr16 90354753 2796067 0.030945433495900322 0.2148109504333613
chr17 81195210 3508787 0.04321421177431526 0.24794605015649818
chr18 78077248 3414424 0.043731356924875224 0.4078788486013445
chr19 59128983 2689162 0.045479591624297 0.3384081520664093
chr20 63025520 2562177 0.04065300849560623 0.22815367625181351
chr21 48129895 1254982 0.026074895862540318 0.18855651562815823
chr22 51304566 1059110 0.0206435817038195 0.15869887703421948
chrMT 16571 3851 0.23239394122261783 0.5605054601965319
chrX 155270560 7592714 0.048899894480962776 0.2668762058522178
chrY 59373566 276697 0.004660272552940479 0.10112124956081157