BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818897.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,323,022 number of mapped reads = 1,282,435 (96.93%) number of supplementary alignments = 20,948 (1.58%) number of secondary alignments = 0 number of mapped bases = 118,541,876 bp number of sequenced bases = 118,461,968 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 222,942 duplication rate = 14.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.179 >>>>>>> ACTG content number of A's = 34,633,235 bp (29.24%) number of C's = 24,934,623 bp (21.05%) number of T's = 34,200,665 bp (28.87%) number of G's = 24,691,758 bp (20.84%) number of N's = 1,687 bp (0%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 744,183 number of insertions = 18,369 mapped reads with insertion percentage = 1.39% number of deletions = 41,009 mapped reads with deletion percentage = 3.12% homopolymer indels = 40.58% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.4962X There is a 2.89% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11898221 0.04773597334387383 0.7336126636508497 chr2 243199373 8177838 0.03362606531062068 0.7453917386312926 chr3 198022430 7468385 0.0377148437174516 0.24279831384332848 chr4 191154276 6115851 0.031994319603920345 0.29781548258747437 chr5 180915260 5293875 0.029261627791928663 0.2283911770575944 chr6 171115067 5889333 0.03441738418043573 0.2570605087831757 chr7 159138663 10597019 0.06658984561155952 1.0500313048594734 chr8 146364022 10413640 0.07114890570580248 0.4105941815880222 chr9 141213431 4399981 0.03115837472995044 0.40481748891090025 chr10 135534747 5553898 0.04097766899583322 0.6931318470852021 chr11 135006516 5252667 0.03890676654451256 0.2945733721905059 chr12 133851895 4628577 0.03457983915730144 0.23505262273992023 chr13 115169878 3624945 0.031474766344720795 0.21912702933092762 chr14 107349540 3500006 0.032603828577188125 0.24570043423796248 chr15 102531392 3298424 0.03216989387991533 0.22315773837097042 chr16 90354753 2973888 0.0329134649950291 0.5408891701292435 chr17 81195210 2939823 0.0362068525963539 0.3046890605664345 chr18 78077248 2293587 0.029375868883083585 0.4487582841395288 chr19 59128983 2009730 0.0339889153852012 0.6210733292244225 chr20 63025520 4558046 0.0723206409086351 0.3571148091446672 chr21 48129895 1161404 0.024130615701530203 0.2293989420159967 chr22 51304566 1052924 0.02052300764029463 0.20288261664727317 chrMT 16571 57749 3.4849435761269687 2.923281226186957 chrX 155270560 4924164 0.031713442651330685 0.2724437803740899 chrY 59373566 457901 0.007712203103987387 0.6003766387848953