BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708651.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,249,187 number of mapped reads = 3,103,149 (95.51%) number of supplementary alignments = 77 (0%) number of secondary alignments = 0 number of mapped bases = 154,781,135 bp number of sequenced bases = 154,765,652 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,141 duplication rate = 0.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.377 >>>>>>> ACTG content number of A's = 47,681,960 bp (30.81%) number of C's = 29,542,562 bp (19.09%) number of T's = 47,719,544 bp (30.83%) number of G's = 29,816,618 bp (19.27%) number of N's = 4,968 bp (0%) GC percentage = 38.35% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 252,810 number of insertions = 10,376 mapped reads with insertion percentage = 0.33% number of deletions = 8,932 mapped reads with deletion percentage = 0.29% homopolymer indels = 48.31% >>>>>>> Coverage mean coverageData = 0.05X std coverageData = 0.2301X There is a 4.75% of reference with a coverageData >= 1X There is a 0.24% 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 12393170 0.04972172165621204 0.2304291343503212 chr2 243199373 14258582 0.05862918898232521 0.24815269778290988 chr3 198022430 12086837 0.06103771678794165 0.2531076916880333 chr4 191154276 10707388 0.056014378668672836 0.24273804419610476 chr5 180915260 11059221 0.06112928782237607 0.25359417252612965 chr6 171115067 10855712 0.06344100604536479 0.2582984584438668 chr7 159138663 8461926 0.053173288253653354 0.23665365536971242 chr8 146364022 8172143 0.05583437027987657 0.24221490418595537 chr9 141213431 6274847 0.04443519965179516 0.21709424501000257 chr10 135534747 6950405 0.05128135148988768 0.2322352119729044 chr11 135006516 6875538 0.05092745301271236 0.23273942522350163 chr12 133851895 6761930 0.05051799976384346 0.23108814779766115 chr13 115169878 6533784 0.05673170896299812 0.24486904935287945 chr14 107349540 4655685 0.04336939869514112 0.21418346937607266 chr15 102531392 4039458 0.03939728039584209 0.20506667246618235 chr16 90354753 2973393 0.03290798658926111 0.18607871211609459 chr17 81195210 2832629 0.03488665156479058 0.1921809246333109 chr18 78077248 6826104 0.08742756916842151 0.3047261186137691 chr19 59128983 1243903 0.021037111360430467 0.14776984874838706 chr20 63025520 2233967 0.03544543543631215 0.19281836692666407 chr21 48129895 1788402 0.037157820518827225 0.19863257084641894 chr22 51304566 963773 0.01878532604680839 0.14052234720075243 chrMT 16571 149 0.008991611852030656 0.0943968366436772 chrX 155270560 5247839 0.03379802971020392 0.1878731729213368 chrY 59373566 584350 0.009841921908480282 0.10223136771028078