BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525259.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,628,478
number of mapped reads = 1,465,706 (90%)
number of supplementary alignments = 5,774 (0.35%)
number of secondary alignments = 0
number of mapped bases = 85,406,085 bp
number of sequenced bases = 85,378,333 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 52,406
duplication rate = 2.59%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.7506
>>>>>>> ACTG content
number of A's = 20,276,675 bp (23.75%)
number of C's = 15,196,676 bp (17.8%)
number of T's = 28,178,254 bp (33%)
number of G's = 21,724,961 bp (25.45%)
number of N's = 1,767 bp (0%)
GC percentage = 43.24%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 429,560
number of insertions = 6,360
mapped reads with insertion percentage = 0.43%
number of deletions = 17,009
mapped reads with deletion percentage = 1.15%
homopolymer indels = 42.69%
>>>>>>> Coverage
mean coverageData = 0.0276X
std coverageData = 0.2615X
There is a 2.49% of reference with a coverageData >= 1X
There is a 0.19% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0% 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 7178568 0.028800602266102277 0.3910599205433532
chr2 243199373 6651444 0.027349758011094873 0.3790075052416239
chr3 198022430 4899943 0.024744383754910997 0.1704327479655218
chr4 191154276 5244176 0.02743425943555665 0.21292414635444754
chr5 180915260 4891544 0.02703776342581604 0.17773751127215165
chr6 171115067 4503910 0.026320943438604385 0.2028082985691017
chr7 159138663 4868087 0.03059022181177933 0.3260027778792219
chr8 146364022 4491229 0.030685334678764158 0.35522139662175245
chr9 141213431 2814820 0.019933089792287535 0.18654506843057087
chr10 135534747 3778111 0.027875589718701434 0.27079917454900404
chr11 135006516 3030549 0.02244742764860327 0.20173392639747406
chr12 133851895 4239432 0.03167255868884038 0.19317229840773195
chr13 115169878 2546929 0.022114541095545833 0.161140361796188
chr14 107349540 2869199 0.02672763199544218 0.1789715693702965
chr15 102531392 3145490 0.030678311672585116 0.19087343477992838
chr16 90354753 2904264 0.032142902321917695 0.20097208550101378
chr17 81195210 3693358 0.045487387741222664 0.24253462910561105
chr18 78077248 1604447 0.020549481969446465 0.3086132938041182
chr19 59128983 2190753 0.03705040893397406 0.32149642494586644
chr20 63025520 2831411 0.044924833622951466 0.23860459606959586
chr21 48129895 1113414 0.023133522314977003 0.19610915350322844
chr22 51304566 807100 0.015731543270437177 0.13496294361087263
chrMT 16571 195506 11.798080984853057 7.519056290744776
chrX 155270560 4602573 0.029642277325463373 0.19804861125457726
chrY 59373566 309828 0.00521828181921901 0.21580100869848898