BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1818738.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,365,313
number of mapped reads = 1,307,039 (95.73%)
number of supplementary alignments = 10,866 (0.8%)
number of secondary alignments = 0
number of mapped bases = 88,744,104 bp
number of sequenced bases = 88,707,427 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 577,924
duplication rate = 38.48%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.7153
>>>>>>> ACTG content
number of A's = 25,030,572 bp (28.22%)
number of C's = 18,732,463 bp (21.12%)
number of T's = 25,861,190 bp (29.15%)
number of G's = 19,077,544 bp (21.51%)
number of N's = 5,658 bp (0.01%)
GC percentage = 42.62%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 435,079
number of insertions = 9,659
mapped reads with insertion percentage = 0.73%
number of deletions = 22,795
mapped reads with deletion percentage = 1.72%
homopolymer indels = 41.77%
>>>>>>> Coverage
mean coverageData = 0.0287X
std coverageData = 0.3777X
There is a 1.36% of reference with a coverageData >= 1X
There is a 0.66% of reference with a coverageData >= 2X
There is a 0.36% of reference with a coverageData >= 3X
There is a 0.2% of reference with a coverageData >= 4X
There is a 0.11% of reference with a coverageData >= 5X
There is a 0.06% of reference with a coverageData >= 6X
There is a 0.03% of reference with a coverageData >= 7X
There is a 0.02% 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% 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 7231422 0.02901265389425048 0.4784752463567218
chr2 243199373 7843498 0.032251308476852036 0.553970965120021
chr3 198022430 6116374 0.03088727877947968 0.31658345294802936
chr4 191154276 5921776 0.030979040196830333 0.35260530503509424
chr5 180915260 5505336 0.03043046783339338 0.31727182140930227
chr6 171115067 5256935 0.030721637154254803 0.33861855101743704
chr7 159138663 4925715 0.030952346256673025 0.3585467184679336
chr8 146364022 4571604 0.031234479194620655 0.35294834994395
chr9 141213431 3782723 0.026787274929960452 0.3342813823327977
chr10 135534747 4253243 0.03138119998113842 0.3862782322813445
chr11 135006516 4196176 0.03108128499516275 0.3372022576509611
chr12 133851895 4086716 0.030531626018443742 0.3258480937509811
chr13 115169878 2871451 0.024932309123397698 0.28493563871416683
chr14 107349540 2782840 0.02592316650821233 0.30926385536788964
chr15 102531392 2551803 0.024888016735401388 0.28515773430575064
chr16 90354753 2609230 0.028877617539389434 0.41504410373095746
chr17 81195210 2405719 0.02962882908979483 0.3277157062865361
chr18 78077248 2394496 0.030668294046429505 0.4400920879336362
chr19 59128983 1729098 0.029242816505063177 0.435261345762148
chr20 63025520 1852923 0.029399567032529047 0.32643084825151586
chr21 48129895 1198804 0.024907679520181792 0.30573732443689694
chr22 51304566 1050221 0.020470322271121055 0.2868531235184578
chrMT 16571 67494 4.073019129805081 5.187005037219664
chrX 155270560 2736059 0.017621234830350326 0.25201482633764016
chrY 59373566 802448 0.01351524009859876 0.5738210879025657