BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008675.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 = 1,609,124 number of mapped reads = 1,401,632 (87.11%) number of supplementary alignments = 7,230 (0.45%) number of secondary alignments = 0 number of mapped bases = 90,366,406 bp number of sequenced bases = 90,323,951 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,797 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7078 >>>>>>> ACTG content number of A's = 24,862,078 bp (27.53%) number of C's = 16,293,393 bp (18.04%) number of T's = 28,113,108 bp (31.12%) number of G's = 21,039,019 bp (23.29%) number of N's = 16,353 bp (0.02%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 710,006 number of insertions = 7,835 mapped reads with insertion percentage = 0.55% number of deletions = 26,015 mapped reads with deletion percentage = 1.84% homopolymer indels = 47.07% >>>>>>> Coverage mean coverageData = 0.0292X std coverageData = 0.3188X There is a 2.63% of reference with a coverageData >= 1X There is a 0.18% 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 0.01% 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 7232593 0.029017351976828174 0.557619597303203 chr2 243199373 8885600 0.03653627840561908 0.40497096410246197 chr3 198022430 7430859 0.037525339932451086 0.2174837156730395 chr4 191154276 4672141 0.02444172894149645 0.1803433251446477 chr5 180915260 4344761 0.02401544789532956 0.16680748215103627 chr6 171115067 4342495 0.025377630831304877 0.2097484660992809 chr7 159138663 5705604 0.035853034658208736 0.49468899280727774 chr8 146364022 7116090 0.04861912034639223 0.3436162524471796 chr9 141213431 2989721 0.021171647617569747 0.27840435892279647 chr10 135534747 5532530 0.04082001200769571 0.46095232016642035 chr11 135006516 3923420 0.029060967694329656 0.2809019394524807 chr12 133851895 4102433 0.03064904684390161 0.189694098216399 chr13 115169878 2672172 0.023202004260176434 0.16136148724182373 chr14 107349540 2882363 0.0268502594421923 0.18692162899227932 chr15 102531392 2323254 0.022658953074586173 0.16165916607927575 chr16 90354753 1912311 0.021164475985009888 0.18845288895122939 chr17 81195210 2636605 0.03247242047899131 0.24238725795875946 chr18 78077248 1393322 0.017845429183159733 0.46830711800657315 chr19 59128983 1536254 0.025981404077252607 0.36885997939255455 chr20 63025520 2122156 0.03367137629328564 0.20200742353479884 chr21 48129895 859662 0.017861289745178126 0.15289238428571925 chr22 51304566 1062096 0.020701783151230634 0.15201411368576523 chrMT 16571 114975 6.938325991189427 4.721784580293996 chrX 155270560 4333399 0.027908696922327066 0.22868200834097588 chrY 59373566 239590 0.004035297458805152 0.10984488357919174