BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080819.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 = 2,441,129 number of mapped reads = 2,212,428 (90.63%) number of supplementary alignments = 22,749 (0.93%) number of secondary alignments = 0 number of mapped bases = 149,371,914 bp number of sequenced bases = 149,315,110 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,108 duplication rate = 4.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2504 >>>>>>> ACTG content number of A's = 42,366,189 bp (28.37%) number of C's = 27,790,900 bp (18.61%) number of T's = 47,227,154 bp (31.63%) number of G's = 31,909,290 bp (21.37%) number of N's = 21,577 bp (0.01%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,215,378 number of insertions = 10,754 mapped reads with insertion percentage = 0.48% number of deletions = 32,250 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.32% >>>>>>> Coverage mean coverageData = 0.0483X std coverageData = 0.3551X There is a 3.88% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 18449690 0.07402063804687573 0.5707395671517028 chr2 243199373 8973529 0.036897829502216685 0.33341817064775386 chr3 198022430 9084594 0.04587659084882455 0.2627900446054418 chr4 191154276 7339128 0.03839374223572169 0.24496642528240478 chr5 180915260 12222366 0.06755851330617439 0.310227180898287 chr6 171115067 11430301 0.06679891607674734 0.3878830288345276 chr7 159138663 10375466 0.06519764464780001 0.4713667938801874 chr8 146364022 7311220 0.04995230316914904 0.5239527988598565 chr9 141213431 5025191 0.03558578645398114 0.26680317787094976 chr10 135534747 6130459 0.045231640857381024 0.45683012204819823 chr11 135006516 5570506 0.04126101587570781 0.26494156366119054 chr12 133851895 5938690 0.04436761989809707 0.25205312548449216 chr13 115169878 6388214 0.05546774999622731 0.2812768435489363 chr14 107349540 4208270 0.03920156527918052 0.24583786265340096 chr15 102531392 4060615 0.03960362695553767 0.23716970194978776 chr16 90354753 3512451 0.038874003673055255 0.2548383868219289 chr17 81195210 3903574 0.04807640746295255 0.27412525047129266 chr18 78077248 1978103 0.025335203925220314 0.3865710178143557 chr19 59128983 2321847 0.03926749425066215 0.424770183330754 chr20 63025520 2757636 0.043754276045639924 0.2530884602503842 chr21 48129895 2278966 0.0473503214582122 0.2695356694415156 chr22 51304566 705089 0.013743201725943847 0.1354939887816433 chrMT 16571 168617 10.175426950697 5.953479886816321 chrX 155270560 8843519 0.056955542634740286 0.29373464070136 chrY 59373566 393873 0.006633810743319679 0.1622230045238844