BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975338.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,585,282 number of mapped reads = 4,520,834 (98.59%) number of supplementary alignments = 16,602 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,259,779 number of mapped paired reads (second in pair) = 2,261,055 number of mapped paired reads (both in pair) = 4,508,234 number of mapped paired reads (singletons) = 12,600 number of mapped bases = 410,194,141 bp number of sequenced bases = 409,956,094 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 177,609 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 83,693.5954 std insert size = 2,809,620.2555 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 53.1383 >>>>>>> ACTG content number of A's = 117,839,221 bp (28.74%) number of C's = 81,987,411 bp (20%) number of T's = 120,311,597 bp (29.35%) number of G's = 89,809,246 bp (21.91%) number of N's = 8,619 bp (0%) GC percentage = 41.91% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 3,221,280 number of insertions = 69,275 mapped reads with insertion percentage = 1.5% number of deletions = 149,787 mapped reads with deletion percentage = 3.25% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 0.1325X std coverageData = 0.8636X There is a 9.03% of reference with a coverageData >= 1X There is a 2.83% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.08% 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% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% 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 33005290 0.13241808532946445 0.9130729991651144 chr2 243199373 35821969 0.14729466017167733 1.1551874853982365 chr3 198022430 24345826 0.12294478963822432 0.4613229491169283 chr4 191154276 25237549 0.1320271224275412 0.6305310056897631 chr5 180915260 24922117 0.137755748188406 0.49515777647405196 chr6 171115067 35154717 0.2054448951593491 1.1408575866868185 chr7 159138663 21144116 0.1328659899574499 0.8489099518338176 chr8 146364022 20939498 0.1430645162238026 0.5523541998074065 chr9 141213431 17153389 0.12147137052423859 1.0921232261752916 chr10 135534747 20587070 0.151895144645085 1.6449915564424316 chr11 135006516 19132182 0.14171302665124696 0.6734199047881827 chr12 133851895 18057222 0.1349044927604499 0.48225791776782534 chr13 115169878 12675064 0.11005537402757343 0.4332990733968618 chr14 107349540 12487314 0.1163238706006565 0.46601521459114664 chr15 102531392 12008044 0.11711578050164383 0.45091138187498553 chr16 90354753 12324372 0.1363998194981508 0.9973462176078097 chr17 81195210 9380593 0.11553135954694864 1.3329960130133944 chr18 78077248 16566706 0.21218352880470379 1.337396722419908 chr19 59128983 5523373 0.09341227803630582 0.5984880786929542 chr20 63025520 9130111 0.14486371552348953 0.5127302140450659 chr21 48129895 5024666 0.1043980253852621 0.552442593214094 chr22 51304566 4406738 0.08589368049619599 0.408129026353294 chrMT 16571 114640 6.918109951119425 38.156880426697654 chrX 155270560 12243315 0.07885148994117108 0.41888036348037855 chrY 59373566 2808260 0.04729815285138844 0.9054948817185298