BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081109.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,764,228 number of mapped reads = 2,503,221 (90.56%) number of supplementary alignments = 28,274 (1.02%) number of secondary alignments = 0 number of mapped bases = 165,442,565 bp number of sequenced bases = 165,383,831 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,845 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2626 >>>>>>> ACTG content number of A's = 47,588,576 bp (28.77%) number of C's = 32,054,972 bp (19.38%) number of T's = 50,378,916 bp (30.46%) number of G's = 35,359,602 bp (21.38%) number of N's = 1,765 bp (0%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,526,235 number of insertions = 13,636 mapped reads with insertion percentage = 0.54% number of deletions = 36,249 mapped reads with deletion percentage = 1.43% homopolymer indels = 45.51% >>>>>>> Coverage mean coverageData = 0.0534X std coverageData = 0.4029X There is a 4.47% of reference with a coverageData >= 1X There is a 0.63% 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 0.01% 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 14129712 0.056688773505603425 0.6002191188912028 chr2 243199373 11257677 0.046289909637225915 0.4280125803269653 chr3 198022430 14045883 0.07093076779231525 0.30667346316181415 chr4 191154276 10493785 0.0548969409399976 0.29021185601559285 chr5 180915260 9742004 0.05384843710806927 0.26852354240192927 chr6 171115067 13356981 0.07805847395074801 0.45795994041001 chr7 159138663 8041951 0.05053423755357301 0.4540499612961922 chr8 146364022 11868912 0.08109173168253056 0.5147939019042178 chr9 141213431 8545640 0.06051577346067032 0.4646021651037715 chr10 135534747 7688137 0.056724472286062554 0.41246429757471925 chr11 135006516 7377346 0.05464436990581995 0.33174186936226535 chr12 133851895 8499346 0.06349813725087718 0.3047963182345725 chr13 115169878 4477188 0.03887464394118747 0.22956692280938631 chr14 107349540 4806416 0.04477351276959361 0.3240286621058089 chr15 102531392 4202049 0.04098304839165746 0.2350648616360685 chr16 90354753 3888150 0.043032047246036965 0.31097529401561574 chr17 81195210 3663633 0.04512129471676962 0.25025271192919796 chr18 78077248 3931119 0.05034909785754744 0.7814929698013019 chr19 59128983 3335175 0.05640507972207132 0.5027034664272273 chr20 63025520 2599242 0.04124110360374655 0.24741612428138923 chr21 48129895 2387809 0.049611764164455376 0.30462015508091117 chr22 51304566 1530835 0.02983818243389877 0.19567370161383782 chrMT 16571 388020 23.415605576006275 12.34434981286635 chrX 155270560 4751428 0.03060095873937725 0.23322273640948188 chrY 59373566 434127 0.007311789222833609 0.17110808873159888