BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1818913.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 = 1,812,740
number of mapped reads = 1,753,286 (96.72%)
number of supplementary alignments = 25,341 (1.4%)
number of secondary alignments = 0
number of mapped bases = 162,524,433 bp
number of sequenced bases = 162,426,991 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 269,912
duplication rate = 12.24%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.2848
>>>>>>> ACTG content
number of A's = 47,238,467 bp (29.08%)
number of C's = 33,751,250 bp (20.78%)
number of T's = 45,370,176 bp (27.93%)
number of G's = 36,064,828 bp (22.2%)
number of N's = 2,270 bp (0%)
GC percentage = 42.98%
>>>>>>> Mismatches and indels
general error rate = 0.0065
number of mismatches = 986,172
number of insertions = 24,450
mapped reads with insertion percentage = 1.35%
number of deletions = 48,728
mapped reads with deletion percentage = 2.71%
homopolymer indels = 40.09%
>>>>>>> Coverage
mean coverageData = 0.0525X
std coverageData = 0.687X
There is a 3.96% of reference with a coverageData >= 1X
There is a 0.79% of reference with a coverageData >= 2X
There is a 0.21% of reference with a coverageData >= 3X
There is a 0.07% 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% 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 15418372 0.06185891107569196 1.0448995456829495
chr2 243199373 12156244 0.0499846847878181 0.8408802927002642
chr3 198022430 9958604 0.050290282772512185 0.2844247936253725
chr4 191154276 7983861 0.04176658334339327 0.38843217957256154
chr5 180915260 6984796 0.03860810856972485 0.2613984365344762
chr6 171115067 7830726 0.04576292513154321 0.30504943767742804
chr7 159138663 13911333 0.08741642500791903 1.7023952121161152
chr8 146364022 15339715 0.10480523007218263 0.5583324324058515
chr9 141213431 5957124 0.04218525077830593 0.595102963121836
chr10 135534747 7630201 0.05629700994682935 0.9392798844887383
chr11 135006516 7030487 0.05207516798670666 0.39375769743004835
chr12 133851895 6258468 0.04675666340024547 0.26901558492802335
chr13 115169878 4858754 0.042187715089877925 0.25135612893191384
chr14 107349540 4778475 0.04451323219456739 0.2868530764049559
chr15 102531392 4422868 0.043136720507998175 0.2538652029675377
chr16 90354753 4193409 0.046410497077004904 0.5440597599623879
chr17 81195210 4399412 0.054183147010765785 0.4789133622623665
chr18 78077248 3058423 0.03917175718078588 0.6859668726782515
chr19 59128983 3070632 0.051931080904943014 0.959423804796281
chr20 63025520 6912613 0.10967958693557785 0.4501038660689757
chr21 48129895 1561485 0.032443141627464596 0.30938186253850897
chr22 51304566 1534895 0.029917317690593075 0.24313053322517628
chrMT 16571 116696 7.042182125399795 5.428980320517573
chrX 155270560 6504592 0.041891985190238255 0.35039758519128517
chrY 59373566 652248 0.010985494790728925 0.77452208788573