BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163155.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 = 82,847,166 number of mapped reads = 80,571,754 (97.25%) number of supplementary alignments = 366,776 (0.44%) number of secondary alignments = 0 number of mapped bases = 7,929,437,457 bp number of sequenced bases = 7,928,492,114 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,947,159 duplication rate = 41.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1757 >>>>>>> ACTG content number of A's = 1,983,808,355 bp (25.02%) number of C's = 1,975,841,860 bp (24.92%) number of T's = 1,989,972,219 bp (25.1%) number of G's = 1,965,167,880 bp (24.79%) number of N's = 13,701,800 bp (0.17%) GC percentage = 49.71% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 50,353,483 number of insertions = 553,399 mapped reads with insertion percentage = 0.68% number of deletions = 405,159 mapped reads with deletion percentage = 0.5% homopolymer indels = 44.76% >>>>>>> Coverage mean coverageData = 2.5614X std coverageData = 30.0127X There is a 9.93% of reference with a coverageData >= 1X There is a 6.42% of reference with a coverageData >= 2X There is a 5.01% of reference with a coverageData >= 3X There is a 4.47% of reference with a coverageData >= 4X There is a 4.09% of reference with a coverageData >= 5X There is a 3.82% of reference with a coverageData >= 6X There is a 3.6% of reference with a coverageData >= 7X There is a 3.42% of reference with a coverageData >= 8X There is a 3.27% of reference with a coverageData >= 9X There is a 3.13% of reference with a coverageData >= 10X There is a 3.01% of reference with a coverageData >= 11X There is a 2.9% of reference with a coverageData >= 12X There is a 2.79% of reference with a coverageData >= 13X There is a 2.7% of reference with a coverageData >= 14X There is a 2.62% of reference with a coverageData >= 15X There is a 2.54% of reference with a coverageData >= 16X There is a 2.46% of reference with a coverageData >= 17X There is a 2.39% of reference with a coverageData >= 18X There is a 2.32% of reference with a coverageData >= 19X There is a 2.26% of reference with a coverageData >= 20X There is a 2.2% of reference with a coverageData >= 21X There is a 2.15% of reference with a coverageData >= 22X There is a 2.09% of reference with a coverageData >= 23X There is a 2.04% of reference with a coverageData >= 24X There is a 1.99% of reference with a coverageData >= 25X There is a 1.95% of reference with a coverageData >= 26X There is a 1.9% of reference with a coverageData >= 27X There is a 1.86% of reference with a coverageData >= 28X There is a 1.82% of reference with a coverageData >= 29X There is a 1.78% of reference with a coverageData >= 30X There is a 1.74% of reference with a coverageData >= 31X There is a 1.71% of reference with a coverageData >= 32X There is a 1.67% of reference with a coverageData >= 33X There is a 1.64% of reference with a coverageData >= 34X There is a 1.61% of reference with a coverageData >= 35X There is a 1.57% of reference with a coverageData >= 36X There is a 1.54% of reference with a coverageData >= 37X There is a 1.51% of reference with a coverageData >= 38X There is a 1.49% of reference with a coverageData >= 39X There is a 1.46% of reference with a coverageData >= 40X There is a 1.43% of reference with a coverageData >= 41X There is a 1.41% of reference with a coverageData >= 42X There is a 1.38% of reference with a coverageData >= 43X There is a 1.36% of reference with a coverageData >= 44X There is a 1.33% of reference with a coverageData >= 45X There is a 1.31% of reference with a coverageData >= 46X There is a 1.29% of reference with a coverageData >= 47X There is a 1.26% of reference with a coverageData >= 48X There is a 1.24% of reference with a coverageData >= 49X There is a 1.22% of reference with a coverageData >= 50X There is a 1.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 925664331 3.71378946734901 35.347974863450915 chr2 243199373 541564331 2.226832759967683 23.058933632722976 chr3 198022430 365454597 1.845521222015102 19.377582454528152 chr4 191154276 291452470 1.5246976217262334 22.246716258409553 chr5 180915260 431388633 2.3844789709834315 35.08557800368922 chr6 171115067 406225554 2.373990561567556 28.243162484805698 chr7 159138663 422183386 2.652927818050099 27.265713401604422 chr8 146364022 413193961 2.823056891672463 59.4250086549485 chr9 141213431 354285941 2.508868586303239 30.89390237326339 chr10 135534747 296601417 2.188379168922638 21.256429904079685 chr11 135006516 415623378 3.078543097875365 28.463836863591617 chr12 133851895 392553355 2.9327440974967147 26.69769198776971 chr13 115169878 132840904 1.1534344422940173 13.780342910862926 chr14 107349540 189810672 1.768155429450373 17.91437875026685 chr15 102531392 292344719 2.851270360203439 24.70889253341831 chr16 90354753 277827161 3.074848325909319 26.816748092235745 chr17 81195210 365735321 4.504395283908989 31.158923197249543 chr18 78077248 121547189 1.5567555480439064 16.79453733316124 chr19 59128983 410363720 6.940145072341258 45.94006854575141 chr20 63025520 174799238 2.773467604868631 26.34961160888583 chr21 48129895 108989922 2.2644953204240315 50.70846721770948 chr22 51304566 156832024 3.0568823835289827 31.16705370211455 chrMT 16571 576 0.034759519642749384 0.21999206110913547 chrX 155270560 434124283 2.7959214096993015 31.114045316610362 chrY 59373566 8030374 0.13525167075193023 7.567510255676428