BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695914.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 14,694,076 number of mapped reads = 13,410,902 (91.27%) number of supplementary alignments = 20,996 (0.14%) number of secondary alignments = 0 number of mapped bases = 1,776,116,410 bp number of sequenced bases = 1,764,856,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,228,524 duplication rate = 20.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.9221 >>>>>>> ACTG content number of A's = 482,552,418 bp (27.34%) number of C's = 397,146,635 bp (22.5%) number of T's = 480,801,175 bp (27.24%) number of G's = 404,356,182 bp (22.91%) number of N's = 0 bp (0%) GC percentage = 45.41% >>>>>>> Mismatches and indels general error rate = 0.0194 number of mismatches = 23,826,531 number of insertions = 9,540,297 mapped reads with insertion percentage = 43.86% number of deletions = 10,118,072 mapped reads with deletion percentage = 47.91% homopolymer indels = 37.23% >>>>>>> Coverage mean coverageData = 0.5737X std coverageData = 1.9397X There is a 19.18% of reference with a coverageData >= 1X There is a 11.23% of reference with a coverageData >= 2X There is a 7.15% of reference with a coverageData >= 3X There is a 4.82% of reference with a coverageData >= 4X There is a 3.38% of reference with a coverageData >= 5X There is a 2.44% of reference with a coverageData >= 6X There is a 1.81% of reference with a coverageData >= 7X There is a 1.37% of reference with a coverageData >= 8X There is a 1.05% of reference with a coverageData >= 9X There is a 0.82% of reference with a coverageData >= 10X There is a 0.64% of reference with a coverageData >= 11X There is a 0.51% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 200041227 0.8025706262934447 2.584943302401997 chr2 243199373 140752896 0.5787551763137152 2.0283036409047415 chr3 198022430 120512811 0.6085816187590466 1.8395283187147138 chr4 191154276 60775608 0.31794009148924296 1.2972497209988636 chr5 180915260 144930622 0.8010967234052009 2.3866610228865643 chr6 171115067 83590133 0.4885024706795691 1.5783494082298115 chr7 159138663 105935653 0.6656814315450168 1.9819930564509372 chr8 146364022 79765634 0.5449811566397103 1.7643339746049829 chr9 141213431 74954884 0.5307914655795029 1.8540681589411592 chr10 135534747 78512709 0.5792810385369296 1.8176663186880544 chr11 135006516 99017759 0.7334294812851848 2.1494949067496463 chr12 133851895 86905993 0.6492697992807648 1.943813849445186 chr13 115169878 33137040 0.2877231492769316 1.1212376833629611 chr14 107349540 37511787 0.34943593610182216 1.2737494418821882 chr15 102531392 68425630 0.6673627331617619 2.0813649962600524 chr16 90354753 74872228 0.8286473651253299 2.640455549861211 chr17 81195210 52567946 0.6474266893330284 1.9480467061465032 chr18 78077248 32912346 0.42153568220027426 1.6904790188965333 chr19 59128983 26633859 0.45043661583017586 1.6856908803915547 chr20 63025520 63284840 1.004114523767515 2.744594081495324 chr21 48129895 15685066 0.32589030165139565 2.1077935921973197 chr22 51304566 22078227 0.43033649285718545 1.510131114375272 chrMT 16571 253794 15.315551264256834 17.468611764725104 chrX 155270560 70882217 0.45650776940586807 1.49903746331609 chrY 59373566 2175501 0.03664090177773725 0.7476554806481919