BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714239.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 319,976 number of mapped reads = 48,825 (15.26%) number of supplementary alignments = 1,186 (0.37%) number of secondary alignments = 0 number of mapped bases = 5,126,013 bp number of sequenced bases = 5,115,001 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,944 duplication rate = 35.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 12.5726 >>>>>>> ACTG content number of A's = 115,485 bp (2.26%) number of C's = 44,513 bp (0.87%) number of T's = 56,456 bp (1.1%) number of G's = 4,898,457 bp (95.77%) number of N's = 90 bp (0%) GC percentage = 96.64% >>>>>>> Mismatches and indels general error rate = 0.0341 number of mismatches = 128,571 number of insertions = 6,469 mapped reads with insertion percentage = 9.01% number of deletions = 2,669 mapped reads with deletion percentage = 5.21% homopolymer indels = 63.45% >>>>>>> Coverage mean coverageData = 0.0017X std coverageData = 6.164X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 17417 6.987745880079473E-5 0.10811429245721238 chr2 243199373 4918464 0.020223999508419785 21.99109168219857 chr3 198022430 4672 2.359328688169315E-5 0.010183558662387321 chr4 191154276 6285 3.287920171872064E-5 0.013268991413933272 chr5 180915260 6533 3.6110828904095764E-5 0.013012767516234544 chr6 171115067 10716 6.262452622012531E-5 0.025960360065298494 chr7 159138663 12647 7.947157379347846E-5 0.06485526961978841 chr8 146364022 7857 5.3681225021269226E-5 0.021375197318928455 chr9 141213431 4236 2.999714665951286E-5 0.015298894330327311 chr10 135534747 11926 8.799219583152356E-5 0.13393311262128896 chr11 135006516 4954 3.6694525173881235E-5 0.02218484895984161 chr12 133851895 8150 6.088819287915199E-5 0.040325758732957864 chr13 115169878 1734 1.5056020116648904E-5 0.004699881607122632 chr14 107349540 7523 7.007948054551514E-5 0.06102670594949568 chr15 102531392 3749 3.6564411414603636E-5 0.013101284495726066 chr16 90354753 10098 1.1175947766688045E-4 0.03741468909443086 chr17 81195210 13174 1.6225095051789385E-4 0.10256058205758323 chr18 78077248 3916 5.015545629886955E-5 0.015015542442726414 chr19 59128983 3120 5.2766001404083E-5 0.015326688979583569 chr20 63025520 3614 5.7341851364336226E-5 0.02250251145850496 chr21 48129895 836 1.736966182868257E-5 0.009554805515167972 chr22 51304566 1475 2.8749877739926696E-5 0.006715834172326608 chrMT 16571 1185 0.07151047009836461 0.3909347929767508 chrX 155270560 59313 3.8199772062392254E-4 0.06294967134467218 chrY 59373566 2419 4.074203661609276E-5 0.011641737570356534