BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238541.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,142,203
number of mapped reads = 2,647,508 (84.26%)
number of supplementary alignments = 25,793 (0.82%)
number of secondary alignments = 0
number of mapped bases = 160,710,649 bp
number of sequenced bases = 160,613,562 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,127,873
duplication rate = 22.19%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.445
>>>>>>> ACTG content
number of A's = 40,072,669 bp (24.95%)
number of C's = 27,201,233 bp (16.94%)
number of T's = 55,541,215 bp (34.58%)
number of G's = 37,794,965 bp (23.53%)
number of N's = 3,480 bp (0%)
GC percentage = 40.47%
>>>>>>> Mismatches and indels
general error rate = 0.0067
number of mismatches = 1,060,013
number of insertions = 10,968
mapped reads with insertion percentage = 0.41%
number of deletions = 57,558
mapped reads with deletion percentage = 2.14%
homopolymer indels = 41.22%
>>>>>>> Coverage
mean coverageData = 0.0519X
std coverageData = 1.1345X
There is a 1.41% of reference with a coverageData >= 1X
There is a 0.76% of reference with a coverageData >= 2X
There is a 0.58% of reference with a coverageData >= 3X
There is a 0.46% of reference with a coverageData >= 4X
There is a 0.37% of reference with a coverageData >= 5X
There is a 0.29% of reference with a coverageData >= 6X
There is a 0.23% of reference with a coverageData >= 7X
There is a 0.19% of reference with a coverageData >= 8X
There is a 0.15% of reference with a coverageData >= 9X
There is a 0.12% of reference with a coverageData >= 10X
There is a 0.1% of reference with a coverageData >= 11X
There is a 0.08% of reference with a coverageData >= 12X
There is a 0.06% of reference with a coverageData >= 13X
There is a 0.05% of reference with a coverageData >= 14X
There is a 0.04% of reference with a coverageData >= 15X
There is a 0.03% of reference with a coverageData >= 16X
There is a 0.03% of reference with a coverageData >= 17X
There is a 0.02% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.02% 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 0.01% of reference with a coverageData >= 26X
There is a 0.01% 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 17245969 0.0691912779627538 0.936769336018572
chr2 243199373 19672021 0.08088845278396338 2.4355896926473317
chr3 198022430 4651243 0.02348846542283114 0.4706358181259686
chr4 191154276 10271235 0.05373269808518435 0.6899750333978251
chr5 180915260 10663808 0.05894366235330287 0.7108107881992346
chr6 171115067 6379495 0.03728190107303642 1.0361414105194404
chr7 159138663 6815747 0.04282898242019288 0.9530451750380238
chr8 146364022 10596377 0.07239741608084534 1.2197633172894433
chr9 141213431 4303515 0.03047525273994653 0.5777295190571553
chr10 135534747 3727613 0.027503006295500003 0.48980786568903434
chr11 135006516 9778207 0.0724276671208966 0.8120910609405977
chr12 133851895 3273879 0.02445896638220923 0.4572520476886359
chr13 115169878 4829215 0.04193123309551478 0.8922873188764838
chr14 107349540 4576292 0.04262982403091806 0.6322382234175286
chr15 102531392 8860991 0.08642222471728464 0.9804643747514238
chr16 90354753 8472441 0.0937686255420343 0.9892102400355725
chr17 81195210 3299779 0.0406400697775152 0.5904908893334463
chr18 78077248 5777448 0.07399656299361371 3.2598043043825613
chr19 59128983 3309447 0.05596996315664689 0.8249371728481667
chr20 63025520 5050209 0.08012958877610213 0.8519975880972874
chr21 48129895 2545271 0.05288336905783817 0.6821548119386864
chr22 51304566 727821 0.014186281197661823 0.3045861780533429
chrMT 16571 22269 1.3438537203548369 2.7375793698655255
chrX 155270560 5341137 0.034398903436684974 0.5434845951574322
chrY 59373566 519220 0.008744969099548442 0.47794887286626847