BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1506337.sorted.bam
outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 10,233,429
number of mapped reads = 8,649,026 (84.52%)
number of supplementary alignments = 172,942 (1.69%)
number of secondary alignments = 0
number of mapped bases = 680,954,935 bp
number of sequenced bases = 680,662,572 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,186,327
duplication rate = 10.02%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.9962
>>>>>>> ACTG content
number of A's = 196,611,551 bp (28.89%)
number of C's = 124,547,703 bp (18.3%)
number of T's = 197,564,966 bp (29.03%)
number of G's = 161,775,894 bp (23.77%)
number of N's = 162,458 bp (0.02%)
GC percentage = 42.07%
>>>>>>> Mismatches and indels
general error rate = 0.0072
number of mismatches = 4,789,112
number of insertions = 55,587
mapped reads with insertion percentage = 0.63%
number of deletions = 150,406
mapped reads with deletion percentage = 1.71%
homopolymer indels = 45.41%
>>>>>>> Coverage
mean coverageData = 0.22X
std coverageData = 1.5323X
There is a 13.04% of reference with a coverageData >= 1X
There is a 4.8% of reference with a coverageData >= 2X
There is a 1.96% of reference with a coverageData >= 3X
There is a 0.87% of reference with a coverageData >= 4X
There is a 0.41% of reference with a coverageData >= 5X
There is a 0.21% of reference with a coverageData >= 6X
There is a 0.11% of reference with a coverageData >= 7X
There is a 0.07% of reference with a coverageData >= 8X
There is a 0.04% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.02% 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 0.01% of reference with a coverageData >= 24X
There is a 0.01% 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 48280450 0.19370242612153812 2.9001257088508274
chr2 243199373 55328146 0.22750118685544474 1.510243461393504
chr3 198022430 42901657 0.21665049257298782 0.6936370248003001
chr4 191154276 42629231 0.2230095600895687 1.0674027039788638
chr5 180915260 52741458 0.2915257563126516 0.8356128968498165
chr6 171115067 24962789 0.14588305657502387 0.6787506102924976
chr7 159138663 32953258 0.20707260811912187 1.674376801605298
chr8 146364022 44704055 0.30543062693371464 2.9144265029845307
chr9 141213431 20193124 0.14299719125158852 1.4420407024346715
chr10 135534747 40523924 0.29899287745009034 1.5718653549972879
chr11 135006516 30460944 0.22562573202022337 1.3523873677055198
chr12 133851895 29038476 0.21694482547296023 0.7327104540779548
chr13 115169878 14115397 0.1225615347096226 0.5109218435999209
chr14 107349540 20105358 0.18728872056647844 0.8559887072598997
chr15 102531392 22939004 0.22372664169038103 0.7348076933075287
chr16 90354753 23684040 0.26212279059630655 0.967533044828697
chr17 81195210 17015754 0.20956598301796375 0.870883327367069
chr18 78077248 12849281 0.1645713870447893 2.498311189900553
chr19 59128983 15639089 0.26449108722198045 2.1635358525969264
chr20 63025520 17285781 0.27426637654080444 0.8605281850886859
chr21 48129895 11578425 0.24056618033344973 0.999745439181075
chr22 51304566 7751266 0.1510833558167123 0.6003323815197928
chrMT 16571 37694 2.27469675939895 2.8448619742952834
chrX 155270560 50918510 0.327934091304881 1.0841389676248088
chrY 59373566 2317824 0.03903797861829623 1.1723999733578927