BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1549060.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,498,311
number of mapped reads = 10,807,740 (86.47%)
number of secondary alignments = 0
number of mapped bases = 428,969,791 bp
number of sequenced bases = 428,923,082 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 510,873
duplication rate = 2.85%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.1003
>>>>>>> ACTG content
number of A's = 128,253,320 bp (29.9%)
number of C's = 86,183,698 bp (20.09%)
number of T's = 128,476,481 bp (29.95%)
number of G's = 86,001,632 bp (20.05%)
number of N's = 7,951 bp (0%)
GC percentage = 40.14%
>>>>>>> Mismatches and indels
general error rate = 0.0033
number of mismatches = 1,399,962
number of insertions = 11,591
mapped reads with insertion percentage = 0.11%
number of deletions = 36,825
mapped reads with deletion percentage = 0.34%
homopolymer indels = 43.9%
>>>>>>> Coverage
mean coverageData = 0.1386X
std coverageData = 1.6615X
There is a 11.09% of reference with a coverageData >= 1X
There is a 1.92% of reference with a coverageData >= 2X
There is a 0.37% of reference with a coverageData >= 3X
There is a 0.09% of reference with a coverageData >= 4X
There is a 0.03% of reference with a coverageData >= 5X
There is a 0.02% 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 0.01% of reference with a coverageData >= 14X
There is a 0.01% 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 35238257 0.141376807241736 4.0206402101538
chr2 243199373 37766019 0.155288307425036 1.0017787997719538
chr3 198022430 26085366 0.13172935005393077 0.4567513901740875
chr4 191154276 30406741 0.15906911232265608 0.5420237486796186
chr5 180915260 27769705 0.15349564763083004 0.5036767094379108
chr6 171115067 30289045 0.177009807090804 0.7120681230132813
chr7 159138663 24665994 0.1549968658464851 1.3634357178143115
chr8 146364022 26904240 0.1838173045012387 3.9079005384178833
chr9 141213431 18337340 0.12985549511929925 0.913318525208999
chr10 135534747 20388058 0.1504267979339645 1.0131606239519768
chr11 135006516 19721721 0.14607977143858744 0.9185378049926384
chr12 133851895 19976736 0.14924507419188948 0.5315837916716885
chr13 115169878 12470135 0.10827601119799744 0.3749893743952969
chr14 107349540 13406123 0.12488291053692452 0.541043816096273
chr15 102531392 12322582 0.1201835043846864 0.4060201401206494
chr16 90354753 10812040 0.11966210565591386 0.5708792187348496
chr17 81195210 10064290 0.12395177006131274 0.5036976640024575
chr18 78077248 12030370 0.15408291542242883 2.083259945336036
chr19 59128983 7313296 0.12368377788604955 2.9791104137368003
chr20 63025520 8435172 0.13383740427687071 0.48484948207282036
chr21 48129895 5643234 0.11725007918675077 0.5602810317673694
chr22 51304566 4047240 0.07888654588755317 0.38759810596121447
chrMT 16571 1470 0.08870919075493332 0.35340166053183947
chrX 155270560 10879668 0.07006909745157099 0.5906676333388083
chrY 59373566 3994949 0.06728497661737211 0.7194255094088882