BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1777246.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 18,250,648
number of mapped reads = 18,148,240 (99.44%)
number of supplementary alignments = 466,704 (2.56%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 9,075,352
number of mapped paired reads (second in pair) = 9,072,888
number of mapped paired reads (both in pair) = 18,119,292
number of mapped paired reads (singletons) = 28,948
number of mapped bases = 1,650,233,122 bp
number of sequenced bases = 1,649,647,385 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 10,217,947
duplication rate = 35.98%
>>>>>>> Insert size
mean insert size = 292,981.0796
std insert size = 5,368,566.9151
median insert size = 195
>>>>>>> Mapping quality
mean mapping quality = 54.2506
>>>>>>> ACTG content
number of A's = 422,184,340 bp (25.59%)
number of C's = 346,651,584 bp (21.01%)
number of T's = 479,774,264 bp (29.08%)
number of G's = 400,974,758 bp (24.31%)
number of N's = 62,439 bp (0%)
GC percentage = 45.32%
>>>>>>> Mismatches and indels
general error rate = 0.0044
number of mismatches = 7,085,625
number of insertions = 95,503
mapped reads with insertion percentage = 0.52%
number of deletions = 333,585
mapped reads with deletion percentage = 1.81%
homopolymer indels = 49.91%
>>>>>>> Coverage
mean coverageData = 0.5331X
std coverageData = 8.7739X
There is a 6.88% of reference with a coverageData >= 1X
There is a 3.43% of reference with a coverageData >= 2X
There is a 1.97% of reference with a coverageData >= 3X
There is a 1.45% of reference with a coverageData >= 4X
There is a 1.15% of reference with a coverageData >= 5X
There is a 0.99% of reference with a coverageData >= 6X
There is a 0.88% of reference with a coverageData >= 7X
There is a 0.8% of reference with a coverageData >= 8X
There is a 0.75% of reference with a coverageData >= 9X
There is a 0.7% of reference with a coverageData >= 10X
There is a 0.67% of reference with a coverageData >= 11X
There is a 0.64% of reference with a coverageData >= 12X
There is a 0.61% of reference with a coverageData >= 13X
There is a 0.58% of reference with a coverageData >= 14X
There is a 0.56% of reference with a coverageData >= 15X
There is a 0.54% of reference with a coverageData >= 16X
There is a 0.52% of reference with a coverageData >= 17X
There is a 0.51% of reference with a coverageData >= 18X
There is a 0.49% of reference with a coverageData >= 19X
There is a 0.48% of reference with a coverageData >= 20X
There is a 0.46% of reference with a coverageData >= 21X
There is a 0.45% of reference with a coverageData >= 22X
There is a 0.44% of reference with a coverageData >= 23X
There is a 0.42% of reference with a coverageData >= 24X
There is a 0.41% of reference with a coverageData >= 25X
There is a 0.4% of reference with a coverageData >= 26X
There is a 0.39% of reference with a coverageData >= 27X
There is a 0.38% of reference with a coverageData >= 28X
There is a 0.37% of reference with a coverageData >= 29X
There is a 0.36% of reference with a coverageData >= 30X
There is a 0.35% of reference with a coverageData >= 31X
There is a 0.35% of reference with a coverageData >= 32X
There is a 0.34% of reference with a coverageData >= 33X
There is a 0.33% of reference with a coverageData >= 34X
There is a 0.32% of reference with a coverageData >= 35X
There is a 0.32% of reference with a coverageData >= 36X
There is a 0.31% of reference with a coverageData >= 37X
There is a 0.3% of reference with a coverageData >= 38X
There is a 0.3% of reference with a coverageData >= 39X
There is a 0.29% of reference with a coverageData >= 40X
There is a 0.28% of reference with a coverageData >= 41X
There is a 0.28% of reference with a coverageData >= 42X
There is a 0.27% of reference with a coverageData >= 43X
There is a 0.27% of reference with a coverageData >= 44X
There is a 0.26% of reference with a coverageData >= 45X
There is a 0.26% of reference with a coverageData >= 46X
There is a 0.25% of reference with a coverageData >= 47X
There is a 0.25% of reference with a coverageData >= 48X
There is a 0.24% of reference with a coverageData >= 49X
There is a 0.24% of reference with a coverageData >= 50X
There is a 0.23% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 163123479 0.6544556573040594 10.29746911910182
chr2 243199373 147730711 0.6074469238043636 9.083681775941082
chr3 198022430 94640070 0.47792601070494894 7.88843315435966
chr4 191154276 79442885 0.41559564694226353 7.4970373365540794
chr5 180915260 87190760 0.4819425403915623 7.638485304892142
chr6 171115067 75639680 0.4420398584772199 7.752824699394907
chr7 159138663 113277001 0.711813200290617 11.296643622298442
chr8 146364022 55304480 0.3778557000845467 7.371977645497873
chr9 141213431 58603995 0.41500298225881926 6.906273248439693
chr10 135534747 73760131 0.5442156541598886 8.56744879038638
chr11 135006516 106710989 0.7904136197396576 11.36904538779921
chr12 133851895 91603888 0.6843675093281272 9.464645860323044
chr13 115169878 52536825 0.4561681049970375 8.283710251806747
chr14 107349540 37747642 0.35163301118942847 6.6723801053654785
chr15 102531392 74975335 0.7312427300314035 9.980343158610866
chr16 90354753 51968224 0.5751576123505091 7.555446078504424
chr17 81195210 69161801 0.8517965653392607 10.435085962825037
chr18 78077248 27962912 0.3581441804916075 7.727355837323933
chr19 59128983 59778059 1.0109772901049219 13.466371570701535
chr20 63025520 49499273 0.7853846029354459 13.722930513114914
chr21 48129895 11674747 0.2425674728773042 5.117373746728105
chr22 51304566 21473762 0.41855459804493816 6.6362904806347265
chrMT 16571 348879 21.053587592782574 12.595013237004023
chrX 155270560 45262673 0.291508403138367 6.062177203920212
chrY 59373566 814921 0.01372531675122899 0.8064915474445518