BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238255.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 = 2,325,413 number of mapped reads = 2,101,165 (90.36%) number of supplementary alignments = 16,003 (0.69%) number of secondary alignments = 0 number of mapped bases = 136,835,189 bp number of sequenced bases = 136,771,312 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,428 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3563 >>>>>>> ACTG content number of A's = 37,418,606 bp (27.36%) number of C's = 27,199,636 bp (19.89%) number of T's = 40,466,029 bp (29.59%) number of G's = 31,653,084 bp (23.14%) number of N's = 33,957 bp (0.02%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,199,664 number of insertions = 11,083 mapped reads with insertion percentage = 0.52% number of deletions = 38,596 mapped reads with deletion percentage = 1.82% homopolymer indels = 44.56% >>>>>>> Coverage mean coverageData = 0.0442X std coverageData = 0.3966X There is a 3.84% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14807851 0.05940948488148401 0.6939339358611379 chr2 243199373 9447115 0.03884514537790359 0.5387803949451218 chr3 198022430 7174985 0.03623319338117404 0.2121071649557746 chr4 191154276 8833630 0.04621204497669725 0.25281330235708493 chr5 180915260 10636034 0.058790142965275564 0.27278679332509614 chr6 171115067 9538206 0.05574147365994369 0.3456723555907348 chr7 159138663 7154733 0.04495911216748126 0.6103101211731511 chr8 146364022 6419157 0.04385747885501534 0.38239644992257166 chr9 141213431 4928916 0.03490401702653907 0.36778208608847546 chr10 135534747 5585273 0.041209159448978794 0.3620104470654135 chr11 135006516 5126304 0.037970789498782416 0.2973622911410015 chr12 133851895 6869867 0.05132439103682469 0.25898047888239634 chr13 115169878 2573889 0.02234863008190388 0.167004092843072 chr14 107349540 3409136 0.03175734148464912 0.2504951212271469 chr15 102531392 3449613 0.033644456909353186 0.21563160663145436 chr16 90354753 4009877 0.04437925916304591 0.26598116917923265 chr17 81195210 4276984 0.05267532407392012 0.29284005920409295 chr18 78077248 3423823 0.04385173770468959 0.627546660440801 chr19 59128983 3070499 0.05192883158501137 0.563040942486646 chr20 63025520 3484221 0.055282701356529865 0.2709688038529437 chr21 48129895 1936228 0.04022921720481626 0.24443656591407062 chr22 51304566 2177297 0.04243865935831131 0.23342884018913093 chrMT 16571 17248 1.0408545048578843 1.2082859550641112 chrX 155270560 8122242 0.05231025121568442 0.2955592685922046 chrY 59373566 362061 0.006098016750417181 0.12535361860193278