BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1549128.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 = 15,431,556
number of mapped reads = 13,603,186 (88.15%)
number of secondary alignments = 0
number of mapped bases = 539,926,113 bp
number of sequenced bases = 539,873,622 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 635,472
duplication rate = 3.47%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.6971
>>>>>>> ACTG content
number of A's = 160,499,457 bp (29.73%)
number of C's = 108,671,131 bp (20.13%)
number of T's = 162,010,432 bp (30.01%)
number of G's = 108,567,738 bp (20.11%)
number of N's = 124,864 bp (0.02%)
GC percentage = 40.24%
>>>>>>> Mismatches and indels
general error rate = 0.0033
number of mismatches = 1,748,163
number of insertions = 14,110
mapped reads with insertion percentage = 0.1%
number of deletions = 42,027
mapped reads with deletion percentage = 0.31%
homopolymer indels = 46.98%
>>>>>>> Coverage
mean coverageData = 0.1744X
std coverageData = 1.0268X
There is a 13.11% of reference with a coverageData >= 1X
There is a 3.01% of reference with a coverageData >= 2X
There is a 0.75% of reference with a coverageData >= 3X
There is a 0.21% of reference with a coverageData >= 4X
There is a 0.07% of reference with a coverageData >= 5X
There is a 0.03% 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% 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 43344981 0.17390119561627893 2.037919239476098
chr2 243199373 46458656 0.19103115039692145 0.9548869949168174
chr3 198022430 38030031 0.19204910777026624 0.5548519620459669
chr4 191154276 37369023 0.19549143122490234 0.5621315063131802
chr5 180915260 34832856 0.19253685952196625 0.5792619859388279
chr6 171115067 33599161 0.19635419363743112 0.7289176248073285
chr7 159138663 31281224 0.19656583391051866 1.6490846877360277
chr8 146364022 28194238 0.1926309322109227 0.9428131670839198
chr9 141213431 23538318 0.1666861135892945 0.9258101190638727
chr10 135534747 25062461 0.1849153929508571 0.8421115509598789
chr11 135006516 24874500 0.1842466625833082 0.8650401482068669
chr12 133851895 24727551 0.18473814659105126 0.5939944389860776
chr13 115169878 17875035 0.15520581692376195 0.48264246440574426
chr14 107349540 16947663 0.15787364342688381 0.7844923094858861
chr15 102531392 15811187 0.15420825458021675 0.48729640715980993
chr16 90354753 14551038 0.16104341517042275 0.6061111685968622
chr17 81195210 13272008 0.16345801679680366 0.5967277453557718
chr18 78077248 14968874 0.19171877062060383 2.047139180395642
chr19 59128983 9230423 0.15610657467252564 1.6967721147499955
chr20 63025520 10930636 0.17343190504417894 0.5782214776922319
chr21 48129895 7203122 0.1496600397736168 0.6159712877011718
chr22 51304566 5446869 0.10616733411213342 0.4779343407226471
chrMT 16571 100705 6.077183030595619 8.03570421907557
chrX 155270560 18423974 0.11865722645683767 0.6464704955961857
chrY 59373566 3851579 0.064870265666711 0.39344193664359073