BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1819005.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 = 955,569
number of mapped reads = 898,825 (94.06%)
number of supplementary alignments = 15,136 (1.58%)
number of secondary alignments = 0
number of mapped bases = 82,892,293 bp
number of sequenced bases = 82,840,357 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 279,838
duplication rate = 26.61%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.0366
>>>>>>> ACTG content
number of A's = 24,395,185 bp (29.45%)
number of C's = 17,382,252 bp (20.98%)
number of T's = 23,959,662 bp (28.92%)
number of G's = 17,099,220 bp (20.64%)
number of N's = 4,038 bp (0%)
GC percentage = 41.62%
>>>>>>> Mismatches and indels
general error rate = 0.007
number of mismatches = 549,764
number of insertions = 14,229
mapped reads with insertion percentage = 1.53%
number of deletions = 26,786
mapped reads with deletion percentage = 2.91%
homopolymer indels = 40.09%
>>>>>>> Coverage
mean coverageData = 0.0268X
std coverageData = 0.391X
There is a 1.66% of reference with a coverageData >= 1X
There is a 0.56% of reference with a coverageData >= 2X
There is a 0.22% of reference with a coverageData >= 3X
There is a 0.09% of reference with a coverageData >= 4X
There is a 0.04% 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% 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 8171017 0.032782333569391586 0.6445032927964524
chr2 243199373 6819170 0.028039422618083804 0.637814397413637
chr3 198022430 4611723 0.023288892071468874 0.22492987558450644
chr4 191154276 4440804 0.023231517980795785 0.2768477317398249
chr5 180915260 4994181 0.027605084280894823 0.25992163875132723
chr6 171115067 3451706 0.02017184144281111 0.245875860683531
chr7 159138663 4008279 0.02518733615350281 0.40191747320380466
chr8 146364022 7635347 0.05216682963248988 0.3706109381402805
chr9 141213431 3619624 0.025632292724337247 0.3380355336851176
chr10 135534747 4229364 0.03120501637856748 0.5054138248466444
chr11 135006516 2880655 0.021337155311822134 0.25131409550754197
chr12 133851895 3747278 0.027995703758994222 0.25157398618567645
chr13 115169878 1708500 0.01483460805610995 0.17903120945802758
chr14 107349540 1956017 0.018221009610288035 0.2102332418243346
chr15 102531392 2122845 0.020704341944367634 0.21624542406841907
chr16 90354753 2735029 0.03026989626101905 0.5133048931956495
chr17 81195210 2848185 0.035078239221254554 0.3001775509991604
chr18 78077248 1955045 0.025039881016298116 0.3812316736967821
chr19 59128983 1658689 0.028052046827864434 0.5473931033995494
chr20 63025520 2154672 0.03418729428967821 0.2991328864805135
chr21 48129895 1130237 0.023483055593618064 0.25479054323791156
chr22 51304566 634903 0.01237517534014419 0.18666857394950728
chrMT 16571 12373 0.7466658620481564 1.243750412615316
chrX 155270560 4995911 0.03217551994402545 0.30499938963905854
chrY 59373566 370739 0.006244176069869207 0.4361620104602332