BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3124955.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,387,544
number of mapped reads = 2,348,953 (98.38%)
number of supplementary alignments = 41,015 (1.72%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 1,176,695
number of mapped paired reads (second in pair) = 1,172,258
number of mapped paired reads (both in pair) = 2,338,038
number of mapped paired reads (singletons) = 10,915
number of mapped bases = 314,471,539 bp
number of sequenced bases = 314,222,802 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 383,072
duplication rate = 14.86%
>>>>>>> Insert size
mean insert size = 100,194.0385
std insert size = 3,055,908.4574
median insert size = 169
>>>>>>> Mapping quality
mean mapping quality = 53.428
>>>>>>> ACTG content
number of A's = 91,551,842 bp (29.14%)
number of C's = 63,649,139 bp (20.26%)
number of T's = 92,030,794 bp (29.29%)
number of G's = 66,956,935 bp (21.31%)
number of N's = 34,092 bp (0.01%)
GC percentage = 41.56%
>>>>>>> Mismatches and indels
general error rate = 0.012
number of mismatches = 3,572,099
number of insertions = 68,869
mapped reads with insertion percentage = 2.74%
number of deletions = 117,135
mapped reads with deletion percentage = 4.77%
homopolymer indels = 44.59%
>>>>>>> Coverage
mean coverageData = 0.1016X
std coverageData = 1.4243X
There is a 5.77% of reference with a coverageData >= 1X
There is a 3.14% of reference with a coverageData >= 2X
There is a 0.42% of reference with a coverageData >= 3X
There is a 0.19% of reference with a coverageData >= 4X
There is a 0.05% of reference with a coverageData >= 5X
There is a 0.03% of reference with a coverageData >= 6X
There is a 0.02% 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 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% 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 25415390 0.1019672083384699 1.6297161674404068
chr2 243199373 28279446 0.11628091656305381 1.6547789932563866
chr3 198022430 21474255 0.10844354854144553 0.4764537732793522
chr4 191154276 20668785 0.10812619750133133 1.229733088293421
chr5 180915260 18649841 0.10308605808045158 0.45665255228094753
chr6 171115067 16560003 0.09677700094054253 0.9044563717595131
chr7 159138663 22554445 0.1417282549370168 2.264958768852617
chr8 146364022 20635844 0.1409898670316671 0.619671201813283
chr9 141213431 13280278 0.09404401483595423 2.3458117579456292
chr10 135534747 16911701 0.12477760407816307 3.2427861319420117
chr11 135006516 14283937 0.10580183403888446 0.9828991077129932
chr12 133851895 14665872 0.1095679071260067 0.45940396090743446
chr13 115169878 8315369 0.07220090135026452 0.3667358948257265
chr14 107349540 9121802 0.08497290253875331 0.4423170234707951
chr15 102531392 8151891 0.07950629403334347 0.38825766805894313
chr16 90354753 9965113 0.11028875260164786 1.8817448904706258
chr17 81195210 7355487 0.09059015919781475 1.3175629249033727
chr18 78077248 8651364 0.11080518616639767 2.191137402128032
chr19 59128983 4005363 0.0677394197698276 0.8111895836614722
chr20 63025520 6313457 0.10017302514917767 0.5644580211712711
chr21 48129895 4091429 0.08500805995940776 0.7377595670757042
chr22 51304566 2803857 0.05465121759338146 0.3387054069345965
chrMT 16571 186712 11.267394846418442 7.138616938893256
chrX 155270560 9669832 0.06227730485418485 0.4727559665847792
chrY 59373566 2460066 0.04143369121538026 1.7827455919853692