BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153399.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 50,787,396 number of mapped reads = 50,176,749 (98.8%) number of supplementary alignments = 356,837 (0.7%) number of secondary alignments = 0 number of mapped bases = 4,851,021,231 bp number of sequenced bases = 4,850,107,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,276,932 duplication rate = 31.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.2445 >>>>>>> ACTG content number of A's = 1,289,164,918 bp (26.58%) number of C's = 1,131,122,176 bp (23.32%) number of T's = 1,313,850,277 bp (27.09%) number of G's = 1,114,035,349 bp (22.97%) number of N's = 1,935,106 bp (0.04%) GC percentage = 46.29% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 15,502,832 number of insertions = 503,113 mapped reads with insertion percentage = 0.99% number of deletions = 426,803 mapped reads with deletion percentage = 0.84% homopolymer indels = 49.12% >>>>>>> Coverage mean coverageData = 1.567X std coverageData = 13.5485X There is a 25.63% of reference with a coverageData >= 1X There is a 13.36% of reference with a coverageData >= 2X There is a 7.27% of reference with a coverageData >= 3X There is a 5.15% of reference with a coverageData >= 4X There is a 3.93% of reference with a coverageData >= 5X There is a 3.31% of reference with a coverageData >= 6X There is a 2.9% of reference with a coverageData >= 7X There is a 2.63% of reference with a coverageData >= 8X There is a 2.43% of reference with a coverageData >= 9X There is a 2.26% of reference with a coverageData >= 10X There is a 2.12% of reference with a coverageData >= 11X There is a 2.01% of reference with a coverageData >= 12X There is a 1.9% of reference with a coverageData >= 13X There is a 1.81% of reference with a coverageData >= 14X There is a 1.73% of reference with a coverageData >= 15X There is a 1.65% of reference with a coverageData >= 16X There is a 1.58% of reference with a coverageData >= 17X There is a 1.52% of reference with a coverageData >= 18X There is a 1.46% of reference with a coverageData >= 19X There is a 1.41% of reference with a coverageData >= 20X There is a 1.36% of reference with a coverageData >= 21X There is a 1.31% of reference with a coverageData >= 22X There is a 1.26% of reference with a coverageData >= 23X There is a 1.22% of reference with a coverageData >= 24X There is a 1.18% of reference with a coverageData >= 25X There is a 1.14% of reference with a coverageData >= 26X There is a 1.11% of reference with a coverageData >= 27X There is a 1.07% of reference with a coverageData >= 28X There is a 1.04% of reference with a coverageData >= 29X There is a 1.01% of reference with a coverageData >= 30X There is a 0.98% of reference with a coverageData >= 31X There is a 0.95% of reference with a coverageData >= 32X There is a 0.93% of reference with a coverageData >= 33X There is a 0.9% of reference with a coverageData >= 34X There is a 0.88% of reference with a coverageData >= 35X There is a 0.85% of reference with a coverageData >= 36X There is a 0.83% of reference with a coverageData >= 37X There is a 0.81% of reference with a coverageData >= 38X There is a 0.79% of reference with a coverageData >= 39X There is a 0.77% of reference with a coverageData >= 40X There is a 0.75% of reference with a coverageData >= 41X There is a 0.73% of reference with a coverageData >= 42X There is a 0.71% of reference with a coverageData >= 43X There is a 0.7% of reference with a coverageData >= 44X There is a 0.68% of reference with a coverageData >= 45X There is a 0.67% of reference with a coverageData >= 46X There is a 0.65% of reference with a coverageData >= 47X There is a 0.64% of reference with a coverageData >= 48X There is a 0.62% of reference with a coverageData >= 49X There is a 0.61% of reference with a coverageData >= 50X There is a 0.59% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 535727633 2.1493532527648145 17.490438937985 chr2 243199373 371410442 1.5271850310239081 12.57782223001211 chr3 198022430 262514882 1.3256825603039009 10.042553128214058 chr4 191154276 205249806 1.0737390253305137 8.969323386024183 chr5 180915260 221169687 1.2225043205310597 9.64528753752919 chr6 171115067 261496265 1.528189595367426 13.233014267629594 chr7 159138663 262670178 1.650574241659929 15.757554607400737 chr8 146364022 210219921 1.4362813902449332 15.642946792513248 chr9 141213431 197245625 1.3967908265043145 12.121640392693333 chr10 135534747 199367513 1.470969750657372 11.346003027089699 chr11 135006516 252278456 1.8686391107226261 13.600101875110509 chr12 133851895 268296581 2.004428708312273 16.751130178432025 chr13 115169878 97686486 0.848194751061558 7.691728713674582 chr14 107349540 153728184 1.4320339332613814 11.916061429240024 chr15 102531392 196894357 1.9203324285307664 15.635741065934605 chr16 90354753 185072389 2.0482861482671533 15.347513936219622 chr17 81195210 219593329 2.7045108818611343 19.262376978719193 chr18 78077248 97615784 1.2502462176945581 10.442598885504772 chr19 59128983 215742245 3.648671667496801 25.824339599147358 chr20 63025520 100640885 1.5968275232001259 11.15639301516826 chr21 48129895 44071103 0.9156700424964567 7.443279234095885 chr22 51304566 71034929 1.3845732366199142 12.520974551661928 chrMT 16571 8522 0.5142719208255386 1.4395768044121804 chrX 155270560 217763311 1.4024764965103493 13.696406729929887 chrY 59373566 3522718 0.05933142031590287 2.348779314885387