BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124937.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 = 4,907,760 number of mapped reads = 4,840,359 (98.63%) number of supplementary alignments = 22,306 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,421,834 number of mapped paired reads (second in pair) = 2,418,525 number of mapped paired reads (both in pair) = 4,824,348 number of mapped paired reads (singletons) = 16,011 number of mapped bases = 445,626,113 bp number of sequenced bases = 445,381,271 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 237,321 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 72,067.055 std insert size = 2,588,530.6479 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 52.8657 >>>>>>> ACTG content number of A's = 131,247,528 bp (29.47%) number of C's = 87,677,905 bp (19.69%) number of T's = 131,077,374 bp (29.43%) number of G's = 95,086,516 bp (21.35%) number of N's = 291,948 bp (0.07%) GC percentage = 41.04% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,884,940 number of insertions = 71,937 mapped reads with insertion percentage = 1.45% number of deletions = 148,962 mapped reads with deletion percentage = 3.02% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.144X std coverageData = 1.3523X There is a 9.48% of reference with a coverageData >= 1X There is a 3.06% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% 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 34655411 0.13903841387019053 1.3751240417601922 chr2 243199373 37726814 0.15512710223969203 1.5827762725025467 chr3 198022430 43134238 0.21782501103536606 0.6480160796547654 chr4 191154276 25786728 0.13490008457880376 0.8093401352653451 chr5 180915260 23366138 0.1291551525283163 0.48218234454727976 chr6 171115067 21877487 0.12785248770641572 0.9318056743926504 chr7 159138663 29485619 0.18528256078159963 2.674139159748668 chr8 146364022 28678734 0.19594114460724507 0.8074264381754757 chr9 141213431 17628238 0.12483400392700607 1.6901896829281775 chr10 135534747 22036909 0.16259232032948717 2.92626550798981 chr11 135006516 19917780 0.14753199023371583 1.06737697701706 chr12 133851895 24447968 0.1826493976794277 0.5767878947900388 chr13 115169878 9309198 0.08083014553510251 0.3708308445377306 chr14 107349540 12762165 0.11888420760815556 0.4877116990994379 chr15 102531392 11741962 0.11452065334292935 0.45391767114208237 chr16 90354753 14217132 0.1573479150565549 2.2257675925503184 chr17 81195210 10397252 0.12805252920708007 1.5222030711451189 chr18 78077248 11794832 0.15106618511963946 1.7776347704807463 chr19 59128983 5589365 0.09452834661472193 0.8632309974935141 chr20 63025520 13455956 0.21350011868208307 0.6513017069369686 chr21 48129895 5443880 0.1131080797080484 0.5787104193107783 chr22 51304566 4340796 0.08460837579251718 0.3982339884875148 chrMT 16571 273854 16.526099812926198 8.9523137066696 chrX 155270560 13568667 0.08738724842623097 0.5950518084467096 chrY 59373566 3988990 0.0671846120881471 1.1634070317070613