BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237571.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 = 1,994,201 number of mapped reads = 1,557,204 (78.09%) number of supplementary alignments = 15,771 (0.79%) number of secondary alignments = 0 number of mapped bases = 101,962,479 bp number of sequenced bases = 101,900,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,648 duplication rate = 4.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7549 >>>>>>> ACTG content number of A's = 28,688,576 bp (28.15%) number of C's = 18,342,720 bp (18%) number of T's = 32,858,158 bp (32.25%) number of G's = 21,820,427 bp (21.41%) number of N's = 190,385 bp (0.19%) GC percentage = 39.41% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 985,104 number of insertions = 8,669 mapped reads with insertion percentage = 0.55% number of deletions = 37,952 mapped reads with deletion percentage = 2.4% homopolymer indels = 46.55% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.3396X There is a 2.59% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 8536376 0.034248163417815516 0.5753262026203279 chr2 243199373 8613882 0.03541901401201392 0.3332326088412125 chr3 198022430 8044332 0.0406233374673768 0.24537750827227747 chr4 191154276 7257815 0.037968363312992276 0.24704986013097893 chr5 180915260 6917114 0.03823399971898446 0.23885070542657813 chr6 171115067 5736881 0.03352645153100399 0.26232579752046115 chr7 159138663 7236055 0.0454701256350256 0.47353527644062615 chr8 146364022 4806046 0.03283625261404746 0.6459013480096494 chr9 141213431 3713224 0.026295119194434134 0.2644152261217579 chr10 135534747 4409925 0.03253722825778396 0.304199350505626 chr11 135006516 4417469 0.032720413287311255 0.26605818584152346 chr12 133851895 4983727 0.037233144887489265 0.24070307339867497 chr13 115169878 3327885 0.02889544608183053 0.2091077203455831 chr14 107349540 2481165 0.023112954186855387 0.20287068232957084 chr15 102531392 2406772 0.02347351336066909 0.18615142994076073 chr16 90354753 2633328 0.02914432182665587 0.21811955850068304 chr17 81195210 2710705 0.033385035890663994 0.24259022258224142 chr18 78077248 2428405 0.03110259470210835 0.4808950625105807 chr19 59128983 1604281 0.027131888941840925 0.3826625546662831 chr20 63025520 1935099 0.030703419821050265 0.2218909655234188 chr21 48129895 1506824 0.031307444157108594 0.22489205130779522 chr22 51304566 907789 0.01769411712789852 0.15861229786481026 chrMT 16571 49687 2.9984309939050147 2.5786043850493057 chrX 155270560 4983625 0.03209639354685138 0.23354606646784715 chrY 59373566 314068 0.005289694070253419 0.11715386423488346