BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR089599.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,656,684
number of mapped reads = 5,328,887 (69.6%)
number of supplementary alignments = 206 (0%)
number of secondary alignments = 0
number of mapped bases = 247,763,635 bp
number of sequenced bases = 247,713,571 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,637,889
duplication rate = 22.88%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 41.1023
>>>>>>> ACTG content
number of A's = 80,462,278 bp (32.48%)
number of C's = 47,903,166 bp (19.34%)
number of T's = 62,761,943 bp (25.34%)
number of G's = 56,555,593 bp (22.83%)
number of N's = 30,591 bp (0.01%)
GC percentage = 42.17%
>>>>>>> Mismatches and indels
general error rate = 0.0093
number of mismatches = 2,273,081
number of insertions = 13,982
mapped reads with insertion percentage = 0.26%
number of deletions = 33,450
mapped reads with deletion percentage = 0.63%
homopolymer indels = 41.13%
>>>>>>> Coverage
mean coverageData = 0.08X
std coverageData = 0.7813X
There is a 3.1% of reference with a coverageData >= 1X
There is a 1.36% of reference with a coverageData >= 2X
There is a 0.85% of reference with a coverageData >= 3X
There is a 0.59% of reference with a coverageData >= 4X
There is a 0.43% of reference with a coverageData >= 5X
There is a 0.32% of reference with a coverageData >= 6X
There is a 0.25% 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 0.04% of reference with a coverageData >= 16X
There is a 0.03% of reference with a coverageData >= 17X
There is a 0.03% 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 0.02% 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 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% 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 19485859 0.07817777513180198 0.8166051026827225
chr2 243199373 20810888 0.08557130613983943 0.8764440883320849
chr3 198022430 16672391 0.08419445716326175 0.7671056159107463
chr4 191154276 16163540 0.08455756438323148 0.7831348480565148
chr5 180915260 15075374 0.08332837152598405 0.7630372282707235
chr6 171115067 14636563 0.0855363776937305 0.8199495609521413
chr7 159138663 13253843 0.08328487088018328 0.8418538394311507
chr8 146364022 12358795 0.08443874957194057 0.874180477650117
chr9 141213431 10113202 0.07161643144270037 0.7119112060165955
chr10 135534747 11509138 0.08491651222103215 0.7817789456432889
chr11 135006516 11559684 0.0856231561445523 0.8365489022685227
chr12 133851895 11339292 0.08471521452871474 0.7748717907310937
chr13 115169878 8184810 0.07106728028313097 0.7186165098596657
chr14 107349540 7554277 0.070370837173592 0.7181866215307755
chr15 102531392 7052798 0.06878671851056113 0.6868262434797364
chr16 90354753 7193751 0.07961674135725876 0.7304590779862865
chr17 81195210 6736766 0.08296999293431226 0.7481065136869642
chr18 78077248 6590990 0.08441626938490455 0.8027222999943692
chr19 59128983 4992342 0.08443138621207133 0.767176366431793
chr20 63025520 5125600 0.08132578676066457 0.733430760419562
chr21 48129895 3121666 0.06485918990681364 0.6729473180429358
chr22 51304566 2834608 0.055250598942791954 0.5947545461856824
chrMT 16571 2023 0.12208074346750347 1.305074063979321
chrX 155270560 14638608 0.09427806533318357 0.8353321602354798
chrY 59373566 756827 0.01274686785698538 0.2682164326333073