BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6004058.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 = 2,502,887
number of mapped reads = 971,241 (38.8%)
number of supplementary alignments = 8,777 (0.35%)
number of secondary alignments = 0
number of mapped bases = 64,331,780 bp
number of sequenced bases = 64,291,279 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 53,925
duplication rate = 4.36%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.5819
>>>>>>> ACTG content
number of A's = 18,150,099 bp (28.23%)
number of C's = 11,919,758 bp (18.54%)
number of T's = 20,241,360 bp (31.48%)
number of G's = 13,931,268 bp (21.67%)
number of N's = 48,794 bp (0.08%)
GC percentage = 40.21%
>>>>>>> Mismatches and indels
general error rate = 0.0101
number of mismatches = 638,974
number of insertions = 5,555
mapped reads with insertion percentage = 0.56%
number of deletions = 23,609
mapped reads with deletion percentage = 2.4%
homopolymer indels = 44.6%
>>>>>>> Coverage
mean coverageData = 0.0208X
std coverageData = 0.2613X
There is a 1.61% of reference with a coverageData >= 1X
There is a 0.32% of reference with a coverageData >= 2X
There is a 0.08% 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% 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 8877376 0.03561626432216592 0.4407841092851637
chr2 243199373 5580144 0.022944730207014145 0.28963634713754927
chr3 198022430 1216678 0.006144142358014696 0.09803401376648627
chr4 191154276 10923821 0.05714662119303049 0.30325808928585757
chr5 180915260 828728 0.004580752336756999 0.08128837294643979
chr6 171115067 4215993 0.02463835052000418 0.2765308046095079
chr7 159138663 4294465 0.026985679777892818 0.31435524051691494
chr8 146364022 1072931 0.007330565157604101 0.3381423617876338
chr9 141213431 835204 0.005914479905243574 0.1765080056202924
chr10 135534747 2342973 0.017286880684552426 0.259763727771679
chr11 135006516 741625 0.005493253377488832 0.1481466694074592
chr12 133851895 3616392 0.027017861794186776 0.21585897607300192
chr13 115169878 487722 0.004234805215301175 0.0757282447456368
chr14 107349540 4852258 0.0452005476688582 0.2745297582027257
chr15 102531392 3678118 0.03587309143330464 0.25218914795492897
chr16 90354753 2347982 0.0259862588523705 0.23453019387900742
chr17 81195210 453402 0.005584097879665561 0.08981205904104982
chr18 78077248 602948 0.007722454561923085 0.4593916321040503
chr19 59128983 360869 0.006103081461759625 0.24149331736198665
chr20 63025520 2743052 0.043522877716835974 0.26157905437055223
chr21 48129895 1694642 0.035209758924261106 0.24417825223605144
chr22 51304566 1311565 0.02556429382913014 0.1964365525664805
chrMT 16571 33988 2.0510530444752884 1.9215145800484374
chrX 155270560 1031651 0.006644215104267029 0.11534469558232684
chrY 59373566 187253 0.0031538109063551953 0.10343766509529176