BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708556.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 = 4,175,563 number of mapped reads = 3,444,562 (82.49%) number of supplementary alignments = 96 (0%) number of secondary alignments = 0 number of mapped bases = 171,773,193 bp number of sequenced bases = 171,757,520 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,097 duplication rate = 0.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5159 >>>>>>> ACTG content number of A's = 53,209,609 bp (30.98%) number of C's = 32,616,381 bp (18.99%) number of T's = 53,023,648 bp (30.87%) number of G's = 32,900,601 bp (19.16%) number of N's = 7,281 bp (0%) GC percentage = 38.15% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 270,099 number of insertions = 11,428 mapped reads with insertion percentage = 0.33% number of deletions = 9,178 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.61% >>>>>>> Coverage mean coverageData = 0.0555X std coverageData = 0.2421X There is a 5.26% of reference with a coverageData >= 1X There is a 0.28% 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 12931659 0.05188215358548696 0.2351531830032967 chr2 243199373 15656210 0.06437602945629305 0.2600380770730402 chr3 198022430 12900918 0.06514877127808198 0.261323392257812 chr4 191154276 13952316 0.0729898189669584 0.2761238559391353 chr5 180915260 11951778 0.0660628517461711 0.2630023110847964 chr6 171115067 11457393 0.0669572422865603 0.2648757421158366 chr7 159138663 9335279 0.05866128836334386 0.248667968969105 chr8 146364022 9103742 0.062199315621430516 0.2552079612061267 chr9 141213431 7048932 0.04991686661872836 0.22978815990674303 chr10 135534747 6913176 0.05100666916063967 0.23107800918117646 chr11 135006516 8324157 0.061657446222817866 0.2559924878129193 chr12 133851895 8034427 0.060024753478462145 0.25152141394205096 chr13 115169878 6172195 0.053592094627381646 0.2377785277415476 chr14 107349540 5254945 0.04895172350063168 0.22800463499271859 chr15 102531392 4564086 0.044514035272241306 0.21748875686223135 chr16 90354753 3085838 0.03415247009750555 0.1897143178472171 chr17 81195210 2857840 0.03519715017671609 0.1926149669055846 chr18 78077248 4467313 0.05721657863760772 0.24502547662399643 chr19 59128983 1454089 0.024591814812712068 0.1603838041915268 chr20 63025520 2640038 0.04188839695412271 0.21010458219387526 chr21 48129895 1859902 0.0386433837015435 0.20303553823856174 chr22 51304566 927904 0.01808618749450098 0.13790466331881696 chrMT 16571 143 0.008629533522418683 0.09249359260837549 chrX 155270560 10624009 0.06842255866147452 0.2685842578510316 chrY 59373566 254904 0.004293223688130843 0.06797433337366839