BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124950.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,491,108 number of mapped reads = 4,438,428 (98.83%) number of supplementary alignments = 22,304 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,221,089 number of mapped paired reads (second in pair) = 2,217,339 number of mapped paired reads (both in pair) = 4,421,430 number of mapped paired reads (singletons) = 16,998 number of mapped bases = 405,577,602 bp number of sequenced bases = 405,352,054 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 227,181 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 89,730.8594 std insert size = 2,827,336.9648 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 52.7873 >>>>>>> ACTG content number of A's = 117,244,849 bp (28.92%) number of C's = 79,136,321 bp (19.52%) number of T's = 119,881,477 bp (29.57%) number of G's = 88,822,538 bp (21.91%) number of N's = 266,869 bp (0.07%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,503,987 number of insertions = 61,367 mapped reads with insertion percentage = 1.35% number of deletions = 133,888 mapped reads with deletion percentage = 2.95% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.131X std coverageData = 1.357X There is a 9.08% of reference with a coverageData >= 1X There is a 2.58% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 27606921 0.1107596879367454 1.2559638391682524 chr2 243199373 30286547 0.12453382024138689 1.4069182635124897 chr3 198022430 45600595 0.2302799485896623 0.6554206465801135 chr4 191154276 21429495 0.11210575796902393 0.8599745793590705 chr5 180915260 24595814 0.13595212476824786 0.48079524048545186 chr6 171115067 22737657 0.13287933902395632 0.9261309781403904 chr7 159138663 23184882 0.14568981266356373 2.0276057381688664 chr8 146364022 21304327 0.14555713015320118 0.6542930538217533 chr9 141213431 18954159 0.1342234861498408 1.6900917975355674 chr10 135534747 16382567 0.12087355724359009 3.412556279769989 chr11 135006516 21321940 0.15793267341259293 1.2043773897367727 chr12 133851895 25700468 0.19200675492864708 0.5688335329414334 chr13 115169878 8736894 0.07586092953923247 0.34055133416269323 chr14 107349540 13395065 0.12477990124596715 0.491743139330892 chr15 102531392 11814090 0.11522412569996124 0.4369108273603754 chr16 90354753 16266279 0.18002682161059086 3.085373627378818 chr17 81195210 8394746 0.10338967040050762 1.1004773142905433 chr18 78077248 9586973 0.12278830575585861 1.6656379211679062 chr19 59128983 3379430 0.057153528245192375 0.8391914068662846 chr20 63025520 9533063 0.15125718915131522 0.5296650936189371 chr21 48129895 3269836 0.06793773391776567 0.5220651010193977 chr22 51304566 4668370 0.09099326558965531 0.40877928725141544 chrMT 16571 41908 2.528996439563092 2.447902935753439 chrX 155270560 14353377 0.09244107189411824 0.5945090404397181 chrY 59373566 3032199 0.051069848154311634 1.2878731989660166