BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6004155.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 = 1,803,582
number of mapped reads = 1,624,842 (90.09%)
number of supplementary alignments = 14,590 (0.81%)
number of secondary alignments = 0
number of mapped bases = 108,110,756 bp
number of sequenced bases = 108,048,806 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 61,540
duplication rate = 3.11%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.2494
>>>>>>> ACTG content
number of A's = 30,547,902 bp (28.27%)
number of C's = 19,735,512 bp (18.27%)
number of T's = 34,437,824 bp (31.87%)
number of G's = 23,309,380 bp (21.57%)
number of N's = 18,188 bp (0.02%)
GC percentage = 39.84%
>>>>>>> Mismatches and indels
general error rate = 0.0095
number of mismatches = 1,007,453
number of insertions = 8,453
mapped reads with insertion percentage = 0.52%
number of deletions = 36,310
mapped reads with deletion percentage = 2.2%
homopolymer indels = 44.34%
>>>>>>> Coverage
mean coverageData = 0.0349X
std coverageData = 0.2796X
There is a 3% of reference with a coverageData >= 1X
There is a 0.38% of reference with a coverageData >= 2X
There is a 0.06% of reference with a coverageData >= 3X
There is a 0.01% 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 6151620 0.024680460073959052 0.34774195716128636
chr2 243199373 6780475 0.027880314477619975 0.2580314048522099
chr3 198022430 7895921 0.03987387186390956 0.22487970929324547
chr4 191154276 10721429 0.05608783242703919 0.2914046022548516
chr5 180915260 7664663 0.04236603921637124 0.23150411719194836
chr6 171115067 6648344 0.038853060204219185 0.24346684408968894
chr7 159138663 3933263 0.02471594850586372 0.28738126499704725
chr8 146364022 2638104 0.018024265553456847 0.37436857686781416
chr9 141213431 5799410 0.04106840233915144 0.29038398212108035
chr10 135534747 6624030 0.04887329741354075 0.42505276545229315
chr11 135006516 4563688 0.03380346471573269 0.23809333467546018
chr12 133851895 6716111 0.05017568858476004 0.25782257526685587
chr13 115169878 3262792 0.028330254895294758 0.18862821880599362
chr14 107349540 4599038 0.04284171129191611 0.23996324782252085
chr15 102531392 3046603 0.029713855830612347 0.1927096674180522
chr16 90354753 3806984 0.04213374364489713 0.2523553072626413
chr17 81195210 2276818 0.02804128470140049 0.20507712617918533
chr18 78077248 3056366 0.03914541147761765 0.4889464851318733
chr19 59128983 1127237 0.019064034975876384 0.26619453155250594
chr20 63025520 2162346 0.034309054490942716 0.2158420868247501
chr21 48129895 1466123 0.030461795106762647 0.22231172721847403
chr22 51304566 1033077 0.020136160980291695 0.1580446021142996
chrMT 16571 7721 0.4659344638223402 0.7447347238345392
chrX 155270560 5825292 0.03751704122146529 0.2355224506761734
chrY 59373566 303301 0.005108350743157317 0.14925279093380436