BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708629.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 = 3,631,112 number of mapped reads = 2,659,742 (73.25%) number of supplementary alignments = 1,017 (0.03%) number of secondary alignments = 0 number of mapped bases = 129,658,381 bp number of sequenced bases = 129,633,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,508 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3826 >>>>>>> ACTG content number of A's = 38,297,186 bp (29.54%) number of C's = 24,575,947 bp (18.96%) number of T's = 40,707,804 bp (31.4%) number of G's = 26,041,176 bp (20.09%) number of N's = 11,424 bp (0.01%) GC percentage = 39.05% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 825,247 number of insertions = 6,245 mapped reads with insertion percentage = 0.23% number of deletions = 16,218 mapped reads with deletion percentage = 0.61% homopolymer indels = 48.16% >>>>>>> Coverage mean coverageData = 0.0419X std coverageData = 0.4024X There is a 3.64% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10348844 0.04151983236182188 0.7309765707425027 chr2 243199373 11235209 0.046197524530624506 0.41719266168042 chr3 198022430 8861699 0.044750986037288804 0.23832971863015587 chr4 191154276 8682366 0.045420726031783876 0.24302159625080422 chr5 180915260 8211344 0.04538779094698811 0.24357876898286707 chr6 171115067 7812622 0.04565712498011645 0.29905041881004657 chr7 159138663 7220710 0.04537370029305826 0.6217928611402344 chr8 146364022 6654148 0.0454630031962363 0.6434043516234643 chr9 141213431 5428262 0.03844012542971213 0.3256901556306416 chr10 135534747 5929817 0.04375126770996961 0.31951416772377583 chr11 135006516 5763063 0.0426872951821081 0.32365147293637747 chr12 133851895 5825870 0.043524748005995734 0.24321507889795813 chr13 115169878 4502993 0.039098704263626986 0.2232483392823455 chr14 107349540 4011738 0.03737079823537204 0.23890460439554148 chr15 102531392 3677381 0.03586590339083663 0.21199028510546195 chr16 90354753 3384880 0.037462113365524886 0.23439193925320514 chr17 81195210 3083241 0.03797318831985286 0.2644670222768986 chr18 78077248 3624261 0.046418913228089186 0.6918191285795897 chr19 59128983 2191742 0.03706713507993195 0.5709767893725869 chr20 63025520 2498833 0.039647955304454446 0.23971426924010344 chr21 48129895 1712706 0.03558507659324833 0.2294581294201391 chr22 51304566 1274881 0.024849269751156262 0.17483184620309944 chrMT 16571 6763 0.40812262386096193 0.7035718715825602 chrX 155270560 7413336 0.04774463362533116 0.27875842583267485 chrY 59373566 301672 0.005080914291049994 0.09578997137331599