BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6004161.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 = 2,738,626
number of mapped reads = 2,342,885 (85.55%)
number of supplementary alignments = 17,874 (0.65%)
number of secondary alignments = 0
number of mapped bases = 159,878,728 bp
number of sequenced bases = 159,801,207 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 99,603
duplication rate = 3.12%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.231
>>>>>>> ACTG content
number of A's = 43,835,564 bp (27.43%)
number of C's = 30,567,848 bp (19.13%)
number of T's = 50,142,951 bp (31.38%)
number of G's = 35,233,247 bp (22.05%)
number of N's = 21,597 bp (0.01%)
GC percentage = 41.18%
>>>>>>> Mismatches and indels
general error rate = 0.0099
number of mismatches = 1,555,371
number of insertions = 14,058
mapped reads with insertion percentage = 0.59%
number of deletions = 45,443
mapped reads with deletion percentage = 1.92%
homopolymer indels = 46.1%
>>>>>>> Coverage
mean coverageData = 0.0516X
std coverageData = 0.4669X
There is a 4.38% of reference with a coverageData >= 1X
There is a 0.56% of reference with a coverageData >= 2X
There is a 0.09% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% 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 15072771 0.06047235083919811 0.9142510128829736
chr2 243199373 12728657 0.052338362730894046 0.5419877302403409
chr3 198022430 9311716 0.04702354172706597 0.2575333478779645
chr4 191154276 8953328 0.04683823028892119 0.2868059892921423
chr5 180915260 11890884 0.06572626322400886 0.2933421552839521
chr6 171115067 9380466 0.05481963782885349 0.3124838275312389
chr7 159138663 7566445 0.04754623959609363 0.5320412518621008
chr8 146364022 3787664 0.025878381505531463 0.4061966302381084
chr9 141213431 7203499 0.05101142964226965 0.45096445064415364
chr10 135534747 8856867 0.06534757467027993 0.5900450091512569
chr11 135006516 5676724 0.04204777790132737 0.35652081472494646
chr12 133851895 8530090 0.06372782395049394 0.29541283816645886
chr13 115169878 5840489 0.050711949178239124 0.2544090368844094
chr14 107349540 5481827 0.05106521183043728 0.292102664369731
chr15 102531392 4908773 0.04787580568495549 0.24998027346769508
chr16 90354753 3252231 0.03599402236205548 0.3039521640131967
chr17 81195210 3883168 0.047825087218815 0.26673363732910066
chr18 78077248 5303300 0.06792375673896703 0.936374243638605
chr19 59128983 2946420 0.04983038521058277 0.594837820615723
chr20 63025520 2921826 0.04635941123532182 0.2608560899339941
chr21 48129895 2005007 0.04165824587815951 0.2801606693260933
chr22 51304566 2083157 0.04060373495801524 0.2296334074143097
chrMT 16571 39290 2.371009595075735 1.9887038034038418
chrX 155270560 11718236 0.07546978641669097 0.3511270339376395
chrY 59373566 535893 0.009025784302731623 0.21677855155005352