BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818757.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 = 1,940,798 number of mapped reads = 1,891,484 (97.46%) number of supplementary alignments = 15,390 (0.79%) number of secondary alignments = 0 number of mapped bases = 128,377,893 bp number of sequenced bases = 128,326,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,100,399 duplication rate = 47.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8239 >>>>>>> ACTG content number of A's = 37,284,957 bp (29.05%) number of C's = 28,220,533 bp (21.99%) number of T's = 36,335,775 bp (28.32%) number of G's = 26,477,189 bp (20.63%) number of N's = 7,870 bp (0.01%) GC percentage = 42.62% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 651,061 number of insertions = 12,932 mapped reads with insertion percentage = 0.67% number of deletions = 32,465 mapped reads with deletion percentage = 1.7% homopolymer indels = 42.34% >>>>>>> Coverage mean coverageData = 0.0415X std coverageData = 0.5678X There is a 1.41% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 10571725 0.042414036753794085 0.6958399726134636 chr2 243199373 11347594 0.04665963509700331 0.8648076696404288 chr3 198022430 8846651 0.044674994645808555 0.4772505928055914 chr4 191154276 8521697 0.04458020599026516 0.512943827042752 chr5 180915260 7923529 0.043796908010966015 0.4755506480788573 chr6 171115067 7699748 0.04499748698342268 0.507591907817953 chr7 159138663 6991333 0.043932334658360175 0.5275901978690385 chr8 146364022 6774733 0.04628687369632409 0.5262181909443996 chr9 141213431 5529939 0.039160149008772405 0.48410148021149707 chr10 135534747 6098617 0.0449967047933472 0.5681286174663531 chr11 135006516 6076633 0.045009923817306716 0.5115287969762777 chr12 133851895 5980597 0.044680704744598496 0.5357192859620026 chr13 115169878 4177181 0.036269735390359624 0.4350509836386142 chr14 107349540 4028766 0.037529420247166406 0.46426168332228124 chr15 102531392 3631945 0.03542276106033945 0.4247764521583896 chr16 90354753 3677502 0.04070070337085643 0.6363726679289217 chr17 81195210 3366902 0.04146675647492013 0.4835414458166877 chr18 78077248 3460728 0.044324410614472474 0.5970468034954988 chr19 59128983 2489146 0.04209688504197679 0.6130270436523025 chr20 63025520 2736159 0.0434135093213035 0.4963921065508593 chr21 48129895 1705648 0.03543843176886216 0.43772307669353616 chr22 51304566 1502109 0.029278271255622747 0.41314945851984675 chrMT 16571 52500 3.168185384104761 5.411430948550977 chrX 155270560 3917743 0.02523171810547988 0.37155262283264423 chrY 59373566 1268768 0.02136924031142074 0.9626717353032919