BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1818804.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 = 1,285,550
number of mapped reads = 1,247,242 (97.02%)
number of supplementary alignments = 8,370 (0.65%)
number of secondary alignments = 0
number of mapped bases = 84,775,064 bp
number of sequenced bases = 84,739,553 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 429,541
duplication rate = 30.03%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.5959
>>>>>>> ACTG content
number of A's = 24,404,456 bp (28.8%)
number of C's = 18,703,572 bp (22.07%)
number of T's = 23,725,907 bp (28%)
number of G's = 17,900,078 bp (21.12%)
number of N's = 5,540 bp (0.01%)
GC percentage = 43.2%
>>>>>>> Mismatches and indels
general error rate = 0.0055
number of mismatches = 445,901
number of insertions = 10,866
mapped reads with insertion percentage = 0.86%
number of deletions = 21,075
mapped reads with deletion percentage = 1.67%
homopolymer indels = 39.35%
>>>>>>> Coverage
mean coverageData = 0.0274X
std coverageData = 0.3741X
There is a 1.58% of reference with a coverageData >= 1X
There is a 0.61% of reference with a coverageData >= 2X
There is a 0.27% of reference with a coverageData >= 3X
There is a 0.12% of reference with a coverageData >= 4X
There is a 0.06% of reference with a coverageData >= 5X
There is a 0.03% 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% 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 7117806 0.02855682353545671 0.5791810740752797
chr2 243199373 7382080 0.030354025624893366 0.5789427659008958
chr3 198022430 5627056 0.02841625567366283 0.2629650336673879
chr4 191154276 5481041 0.028673389445915402 0.3084590615532626
chr5 180915260 5143586 0.028430912903643395 0.2752491444763405
chr6 171115067 4969346 0.029040961074456407 0.2989443055731888
chr7 159138663 4779091 0.030030986247509193 0.3316974638846228
chr8 146364022 4375914 0.029897470294988203 0.29796923781519385
chr9 141213431 3664498 0.025950067030097158 0.30194345885508395
chr10 135534747 4183752 0.030868482751511685 0.42134003144968446
chr11 135006516 3976493 0.029454082053343263 0.296367001794061
chr12 133851895 3907739 0.02919449888998583 0.2935309933063997
chr13 115169878 2661739 0.023111416337525337 0.23905557312357734
chr14 107349540 2654903 0.024731386832211856 0.2917190971902883
chr15 102531392 2479081 0.024178751030708722 0.24595336634927958
chr16 90354753 2574665 0.028495069871974525 0.4359119963551003
chr17 81195210 2269076 0.027945934249077008 0.28048141386942826
chr18 78077248 2252964 0.02885557646703941 0.36698807225411106
chr19 59128983 1806325 0.030548893425073793 0.49457699476198336
chr20 63025520 1832672 0.029078252745871832 0.2850256386084874
chr21 48129895 1129204 0.023461592841621616 0.2643286711913788
chr22 51304566 1031465 0.0201047407749244 0.2458410220835263
chrMT 16571 46295 2.7937360448977127 3.177195139136198
chrX 155270560 2608132 0.01679733749913699 0.2322441371938658
chrY 59373566 820141 0.013813234664059086 0.6586577766778887