BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054626.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 4,922,274 number of mapped reads = 3,614,568 (73.43%) number of supplementary alignments = 123 (0%) number of secondary alignments = 0 number of mapped bases = 167,470,180 bp number of sequenced bases = 167,433,885 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 760,157 duplication rate = 15.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9052 >>>>>>> ACTG content number of A's = 51,245,121 bp (30.61%) number of C's = 34,622,176 bp (20.68%) number of T's = 48,168,064 bp (28.77%) number of G's = 33,390,849 bp (19.94%) number of N's = 7,675 bp (0%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,144,084 number of insertions = 7,833 mapped reads with insertion percentage = 0.22% number of deletions = 25,033 mapped reads with deletion percentage = 0.69% homopolymer indels = 43.72% >>>>>>> Coverage mean coverageData = 0.0541X std coverageData = 0.5303X There is a 2.71% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 11187350 0.044883940329280066 0.4988116874357239 chr2 243199373 14095581 0.05795895287937276 0.5740164187432563 chr3 198022430 13354859 0.06744114290487194 0.5716416915379073 chr4 191154276 10537870 0.0551275661759196 0.5155582502649962 chr5 180915260 10112329 0.055895389919015125 0.49915027285312297 chr6 171115067 9087954 0.05311019163496573 0.5195041431859044 chr7 159138663 8790159 0.055235847997541616 0.5629769730167232 chr8 146364022 10337982 0.07063198905534313 0.6211057246217142 chr9 141213431 6388790 0.045242084656947394 0.469798090106407 chr10 135534747 6711645 0.04951973680963156 0.4745647442730833 chr11 135006516 8805804 0.06522502958301657 0.6106729559740142 chr12 133851895 8536358 0.06377465182693155 0.6505857300633624 chr13 115169878 6013385 0.05221317504564865 0.4891780681155974 chr14 107349540 3697520 0.034443743308075654 0.42985194706442753 chr15 102531392 4921045 0.04799549585750284 0.45969538269151966 chr16 90354753 5690196 0.06297616684315434 0.5683925193866802 chr17 81195210 3747401 0.0461529811918708 0.4364967144868407 chr18 78077248 5171566 0.06623653026295188 0.5796644768410942 chr19 59128983 3907541 0.06608503650401022 0.6530366850943813 chr20 63025520 3607544 0.05723941666804177 0.5108517348764641 chr21 48129895 1911550 0.039716479747150917 0.4634402197887094 chr22 51304566 2320800 0.04523573983648941 0.45464655124816294 chrMT 16571 24179 1.4591153219479813 3.1833592625889287 chrX 155270560 8165349 0.052587876285111614 0.5170522886517027 chrY 59373566 345423 0.005817791035155275 0.14955813565272041