BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083753.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 = 1,696,497 number of mapped reads = 1,251,226 (73.75%) number of supplementary alignments = 9,569 (0.56%) number of secondary alignments = 0 number of mapped bases = 79,482,573 bp number of sequenced bases = 79,460,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,452 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5813 >>>>>>> ACTG content number of A's = 23,462,453 bp (29.53%) number of C's = 15,167,713 bp (19.09%) number of T's = 22,630,478 bp (28.48%) number of G's = 18,189,347 bp (22.89%) number of N's = 10,883 bp (0.01%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 666,030 number of insertions = 5,789 mapped reads with insertion percentage = 0.46% number of deletions = 13,538 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.43% >>>>>>> Coverage mean coverageData = 0.0257X std coverageData = 0.2811X There is a 2.41% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 8401099 0.03370542856139965 0.6435504274092879 chr2 243199373 6795569 0.027942378782366353 0.24483622049577355 chr3 198022430 6480899 0.032728105598946546 0.1886566778913457 chr4 191154276 3776883 0.019758297219571484 0.14793576113415735 chr5 180915260 3840573 0.02122857408490583 0.15162476619205661 chr6 171115067 5313188 0.03105038085278604 0.22591966972772312 chr7 159138663 5562342 0.03495280087906733 0.42719111763718837 chr8 146364022 5249826 0.03586828189239019 0.2585455801390648 chr9 141213431 3153988 0.0223349009911104 0.19569051822341135 chr10 135534747 3641359 0.026866608604803017 0.2504932713077431 chr11 135006516 2897827 0.021464349172598454 0.18597250321450665 chr12 133851895 2786337 0.020816567445683155 0.1502175960918827 chr13 115169878 2382702 0.020688586645893643 0.14786831321826374 chr14 107349540 1691228 0.015754403791576565 0.13357036658507787 chr15 102531392 2012621 0.01962931508820245 0.14551311914039386 chr16 90354753 2221309 0.02458430714762731 0.1719825196863534 chr17 81195210 1706633 0.021018887690542335 0.15809339406051945 chr18 78077248 2229341 0.028553017135030168 0.36559221271224607 chr19 59128983 2231082 0.03773246023866164 0.4487598613187083 chr20 63025520 1676414 0.026598971337324945 0.17198506375408665 chr21 48129895 1215303 0.025250481016008866 0.16772977133191513 chr22 51304566 630352 0.01228646978516493 0.11419963693421283 chrMT 16571 7521 0.4538651861686078 0.7509729639375965 chrX 155270560 3409193 0.021956467472004994 0.16624682529964216 chrY 59373566 168984 0.002846115053961893 0.07028491170683233