BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081201.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 = 5,098,912 number of mapped reads = 3,995,395 (78.36%) number of supplementary alignments = 43,612 (0.86%) number of secondary alignments = 0 number of mapped bases = 264,745,706 bp number of sequenced bases = 264,661,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 384,773 duplication rate = 7.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2295 >>>>>>> ACTG content number of A's = 74,151,178 bp (28.02%) number of C's = 49,990,988 bp (18.89%) number of T's = 83,130,164 bp (31.41%) number of G's = 57,238,360 bp (21.63%) number of N's = 150,852 bp (0.06%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 2,725,602 number of insertions = 19,567 mapped reads with insertion percentage = 0.49% number of deletions = 54,488 mapped reads with deletion percentage = 1.35% homopolymer indels = 44.63% >>>>>>> Coverage mean coverageData = 0.0855X std coverageData = 0.9864X There is a 6% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.16% 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 0.01% 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 19143445 0.07680400122252855 1.8654336006253132 chr2 243199373 19899263 0.08182283841661056 0.7227126060527019 chr3 198022430 17719498 0.08948227733595633 0.401849481849419 chr4 191154276 18572738 0.09716098634382628 0.425671085808301 chr5 180915260 17613680 0.0973587302696301 0.4344080625494837 chr6 171115067 14886301 0.08699585174460411 0.6142617424542235 chr7 159138663 15277963 0.09600409298399094 1.3334959978111849 chr8 146364022 14677035 0.10027761467227239 1.6202559252429678 chr9 141213431 11765721 0.08331871066853407 0.7730545366415559 chr10 135534747 12618008 0.093097956644284 0.8376599812535627 chr11 135006516 12445215 0.09218232844405821 0.7076929599529274 chr12 133851895 12042915 0.08997194249659297 0.44391773973716847 chr13 115169878 8673679 0.07531204469974345 0.3629444353380176 chr14 107349540 8558414 0.0797247384571932 2.121491989267498 chr15 102531392 7279421 0.07099699768047624 0.3522369842303166 chr16 90354753 6682193 0.07395508014946375 0.4458933348559804 chr17 81195210 6108571 0.07523314491088821 0.4513299631268147 chr18 78077248 7728129 0.09898055064645721 1.6579305758335956 chr19 59128983 4417726 0.07471337702527371 1.1786801229594186 chr20 63025520 4984618 0.07908888336026422 0.41794251396396737 chr21 48129895 3664598 0.07613974640917043 0.4128671642137341 chr22 51304566 2550534 0.049713586895949964 0.2953831121789836 chrMT 16571 155954 9.411260636050933 6.939284061142923 chrX 155270560 16648352 0.10722156215576217 0.5120945738654965 chrY 59373566 631735 0.010640004341325903 0.18886754637038405