BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714189.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 = 57,884 number of mapped reads = 15,665 (27.06%) number of supplementary alignments = 530 (0.92%) number of secondary alignments = 0 number of mapped bases = 1,805,051 bp number of sequenced bases = 1,768,945 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,074 duplication rate = 49.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 27.1105 >>>>>>> ACTG content number of A's = 371,466 bp (21%) number of C's = 324,169 bp (18.33%) number of T's = 345,416 bp (19.53%) number of G's = 727,873 bp (41.15%) number of N's = 21 bp (0%) GC percentage = 59.47% >>>>>>> Mismatches and indels general error rate = 0.0392 number of mismatches = 64,259 number of insertions = 1,122 mapped reads with insertion percentage = 5.72% number of deletions = 4,588 mapped reads with deletion percentage = 27.88% homopolymer indels = 32.22% >>>>>>> Coverage mean coverageData = 0.0006X std coverageData = 0.5315X 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 31570 1.2665966437050522E-4 0.09719356400663472 chr2 243199373 476121 0.0019577394222969483 1.773156918148771 chr3 198022430 25724 1.2990447597274713E-4 0.046193480294521146 chr4 191154276 23571 1.233087770424764E-4 0.05026893314644348 chr5 180915260 26740 1.4780400503528558E-4 0.05575041350314942 chr6 171115067 21284 1.2438413737114103E-4 0.0447580164638275 chr7 159138663 50751 3.1891055915180086E-4 0.15928536746228675 chr8 146364022 54954 3.754611225428063E-4 0.20184171817159147 chr9 141213431 10198 7.221692673128239E-5 0.039964116678614006 chr10 135534747 20978 1.5477949724582434E-4 0.14170681348095296 chr11 135006516 9374 6.94336857044737E-5 0.02076759637404875 chr12 133851895 21594 1.6132756282606235E-4 0.04606832118604593 chr13 115169878 2651 2.3018171470147775E-5 0.007575240363179051 chr14 107349540 13067 1.2172385647856526E-4 0.04375892151262622 chr15 102531392 26583 2.592669374858385E-4 0.0856402333359947 chr16 90354753 8686 9.613218687012513E-5 0.03154505794751273 chr17 81195210 42366 5.217795483255724E-4 0.13467406567428716 chr18 78077248 11397 1.4597082110271098E-4 0.0487033302441991 chr19 59128983 20566 3.478158925885805E-4 0.15623388038871455 chr20 63025520 46559 7.38732500739383E-4 0.2647865072872607 chr21 48129895 2740 5.6929274414581624E-5 0.016372630592063706 chr22 51304566 2196 4.280320780805358E-5 0.012064838477349857 chrMT 16571 0 0.0 0.0 chrX 155270560 845855 0.005447619948044239 0.7344174320315798 chrY 59373566 9526 1.6044176965890848E-4 0.031221555136801797