BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927060.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 21,861,440 number of mapped reads = 21,276,264 (97.32%) number of supplementary alignments = 402,553 (1.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,686,980 number of mapped paired reads (second in pair) = 10,589,284 number of mapped paired reads (both in pair) = 20,919,148 number of mapped paired reads (singletons) = 357,116 number of mapped bases = 1,916,090,949 bp number of sequenced bases = 1,914,724,465 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,688,127 duplication rate = 6.23% >>>>>>> Insert size mean insert size = 207,198.827 std insert size = 4,455,481.3196 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 53.0373 >>>>>>> ACTG content number of A's = 549,939,765 bp (28.72%) number of C's = 365,672,443 bp (19.1%) number of T's = 563,049,444 bp (29.41%) number of G's = 435,801,976 bp (22.76%) number of N's = 260,837 bp (0.01%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 19,964,217 number of insertions = 312,730 mapped reads with insertion percentage = 1.45% number of deletions = 943,967 mapped reads with deletion percentage = 4.33% homopolymer indels = 51.82% >>>>>>> Coverage mean coverageData = 0.619X std coverageData = 2.4492X There is a 30.07% of reference with a coverageData >= 1X There is a 14.28% of reference with a coverageData >= 2X There is a 7.04% of reference with a coverageData >= 3X There is a 3.81% of reference with a coverageData >= 4X There is a 2.16% of reference with a coverageData >= 5X There is a 1.28% of reference with a coverageData >= 6X There is a 0.79% of reference with a coverageData >= 7X There is a 0.5% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 0.01% 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 153153746 0.6144568281737601 3.8472134737430737 chr2 243199373 176262549 0.7247656390956239 4.082451770204832 chr3 198022430 137196706 0.6928341703513082 1.3968817532587239 chr4 191154276 116558301 0.6097603644503354 2.0912889099736613 chr5 180915260 114645423 0.63369680921333 1.3064482801100221 chr6 171115067 111474957 0.6514619603894962 1.432242908628261 chr7 159138663 97255045 0.6111339831980366 1.9516360030507889 chr8 146364022 95363793 0.6515521485191217 1.6309772368182314 chr9 141213431 80100998 0.5672335657647183 2.9602193249344713 chr10 135534747 92291733 0.6809451822712297 3.9336716442044075 chr11 135006516 93486479 0.6924590143486111 2.3481922417936163 chr12 133851895 88191574 0.6588743028255222 1.371463887151614 chr13 115169878 56797865 0.49316597348483776 1.1502508322798892 chr14 107349540 57837013 0.5387728070376454 1.2903663335783726 chr15 102531392 54802435 0.5344942064182646 1.2550297211685866 chr16 90354753 56377471 0.6239568935571104 2.948187311576009 chr17 81195210 46864777 0.5771864744237991 1.9293348868099458 chr18 78077248 50288785 0.6440901323776166 3.0458567313366705 chr19 59128983 30470472 0.5153221052356 2.216454200681558 chr20 63025520 42022521 0.6667540545480625 1.458919560430525 chr21 48129895 24020576 0.49907808857675673 1.7047758994912348 chr22 51304566 21565128 0.42033545318364063 1.1568389270212904 chrMT 16571 384668 23.21332448252972 16.5418223887812 chrX 155270560 114424424 0.7369357333418518 1.710146980112242 chrY 59373566 4253510 0.07163979337202013 1.7431657652179877