BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505987.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,207,274 number of mapped reads = 4,525,141 (72.9%) number of supplementary alignments = 237 (0%) number of secondary alignments = 0 number of mapped bases = 211,670,472 bp number of sequenced bases = 211,628,612 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 432,628 duplication rate = 7.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4471 >>>>>>> ACTG content number of A's = 63,907,117 bp (30.2%) number of C's = 42,138,786 bp (19.91%) number of T's = 63,376,462 bp (29.95%) number of G's = 42,205,292 bp (19.94%) number of N's = 955 bp (0%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,116,310 number of insertions = 9,808 mapped reads with insertion percentage = 0.22% number of deletions = 30,790 mapped reads with deletion percentage = 0.68% homopolymer indels = 44.93% >>>>>>> Coverage mean coverageData = 0.0684X std coverageData = 0.6714X There is a 4.8% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 16539060 0.06635514059561762 1.0416942217043748 chr2 243199373 17514593 0.07201742662387538 0.5597168525477908 chr3 198022430 14996071 0.07572915351053919 0.3765612255387005 chr4 191154276 14729696 0.07705658648200996 0.3800583759261664 chr5 180915260 12945529 0.07155576041512474 0.368886527592417 chr6 171115067 11534665 0.06740882145696732 0.4310195141029072 chr7 159138663 12406225 0.0779585850862653 1.012465964642781 chr8 146364022 11428454 0.07808239923879653 1.2549481279724357 chr9 141213431 8996539 0.06370880543225382 0.5259618996918646 chr10 135534747 9264333 0.06835393288482694 0.6425701619408496 chr11 135006516 9872097 0.0731231150354254 0.6306677917688386 chr12 133851895 9528858 0.0711895636591473 0.3903391870308499 chr13 115169878 7505132 0.06516575453869979 0.34875996494067585 chr14 107349540 6801219 0.06335582807341326 1.1317241677133105 chr15 102531392 5889908 0.05744492379465598 0.32452525518242276 chr16 90354753 5514561 0.061032328869295896 0.3825020484330902 chr17 81195210 4832762 0.05952028450939409 0.39355313098452976 chr18 78077248 5935423 0.07601987969657947 1.1051513558531398 chr19 59128983 3256920 0.05508161708108526 0.7795438432551962 chr20 63025520 4042123 0.06413470289495429 0.3663189698812824 chr21 48129895 2806477 0.058310474186573646 0.35272893652194187 chr22 51304566 1994377 0.038873284689709686 0.26802145174382114 chrMT 16571 61608 3.717820288455736 3.7154505618414877 chrX 155270560 12677519 0.08164792475791934 0.46895960894691335 chrY 59373566 596323 0.010043577305092304 0.14783871485275663