BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506344.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 = 5,982,145 number of mapped reads = 4,092,356 (68.41%) number of supplementary alignments = 65,106 (1.09%) number of secondary alignments = 0 number of mapped bases = 316,605,668 bp number of sequenced bases = 316,468,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 595,121 duplication rate = 10.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3715 >>>>>>> ACTG content number of A's = 91,168,765 bp (28.81%) number of C's = 58,855,136 bp (18.6%) number of T's = 86,954,345 bp (27.48%) number of G's = 79,411,254 bp (25.09%) number of N's = 79,449 bp (0.03%) GC percentage = 43.69% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 2,273,015 number of insertions = 28,563 mapped reads with insertion percentage = 0.68% number of deletions = 65,673 mapped reads with deletion percentage = 1.57% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.1023X std coverageData = 0.7128X There is a 6.23% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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% 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 22672843 0.09096403815980864 0.9615553448590735 chr2 243199373 24279354 0.09983312744807117 0.7964447559248745 chr3 198022430 18369758 0.09276604675541049 0.46479662553133066 chr4 191154276 19857710 0.10388315875288084 0.8160692044443367 chr5 180915260 24081827 0.13311108747819284 0.56987397783168 chr6 171115067 11525536 0.06735547139165717 0.40917486969077504 chr7 159138663 14766199 0.09278825598779851 0.7827615232563376 chr8 146364022 19672955 0.13441113964468673 0.9631339033298147 chr9 141213431 9548701 0.0676189292504337 0.5758501511405004 chr10 135534747 18818265 0.13884457983309623 0.9790467157134723 chr11 135006516 12595297 0.09329399330621939 0.599708851873542 chr12 133851895 14070086 0.10511682333671854 0.5255604952698357 chr13 115169878 6826646 0.059274578722745545 0.3662687580810573 chr14 107349540 9443508 0.08796971090886836 0.489496591672158 chr15 102531392 12233782 0.11931742816873099 0.5427321419785704 chr16 90354753 11520980 0.12750828946430742 0.7123857419976024 chr17 81195210 8675376 0.10684590876727827 0.5698068007860732 chr18 78077248 6009661 0.07697070726673154 0.8283637299747473 chr19 59128983 8093123 0.13687235242994117 0.8142937081814429 chr20 63025520 9536463 0.15131113555270945 0.6833877652005288 chr21 48129895 5466482 0.11357768389064635 0.7996947636167795 chr22 51304566 3822661 0.07450917721436334 0.49057479315221086 chrMT 16571 461211 27.832418079777927 15.639318009024159 chrX 155270560 22936736 0.14772108762923247 0.6350266505081997 chrY 59373566 1320508 0.022240671884184958 0.8645057798747731