BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708648.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,390,026 number of mapped reads = 4,167,744 (94.94%) number of supplementary alignments = 129 (0%) number of secondary alignments = 0 number of mapped bases = 207,870,315 bp number of sequenced bases = 207,850,062 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,541 duplication rate = 0.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1407 >>>>>>> ACTG content number of A's = 64,075,117 bp (30.83%) number of C's = 39,692,686 bp (19.1%) number of T's = 64,049,948 bp (30.82%) number of G's = 40,025,304 bp (19.26%) number of N's = 7,007 bp (0%) GC percentage = 38.35% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 338,727 number of insertions = 14,256 mapped reads with insertion percentage = 0.34% number of deletions = 11,865 mapped reads with deletion percentage = 0.28% homopolymer indels = 49.39% >>>>>>> Coverage mean coverageData = 0.0671X std coverageData = 0.2749X There is a 6.14% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% 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 17506697 0.07023732550700446 0.2819834120444228 chr2 243199373 19654907 0.08081808253675062 0.3009489939606523 chr3 198022430 15684583 0.0792060929663372 0.29612883824308694 chr4 191154276 12930570 0.06764468088592483 0.27413262013105416 chr5 180915260 14278667 0.07892461365613934 0.296129513744868 chr6 171115067 16638707 0.09723694874864526 0.3322463842321621 chr7 159138663 13913377 0.08742926915252518 0.3135477411018085 chr8 146364022 11504427 0.07860146805749844 0.29734214863243774 chr9 141213431 6800545 0.048157919199626274 0.23122679807975322 chr10 135534747 9627664 0.0710346550467977 0.2827196086089355 chr11 135006516 8020368 0.0594072659426305 0.25873663302757915 chr12 133851895 12662725 0.09460250824241226 0.32491505851894575 chr13 115169878 4754855 0.04128557816133139 0.2125309740807577 chr14 107349540 6096677 0.05679276315483047 0.2522318803825771 chr15 102531392 5403261 0.052698601809677954 0.2433529222179811 chr16 90354753 4466278 0.04943047102347787 0.23380961518063 chr17 81195210 4044713 0.04981467502824366 0.2351134765114707 chr18 78077248 8724135 0.11173722465218036 0.3548663687432382 chr19 59128983 1611109 0.02724736530645217 0.17138294255080927 chr20 63025520 2212572 0.03510596977224464 0.1936414248159151 chr21 48129895 2633190 0.05471007156778547 0.24839073963222658 chr22 51304566 1664284 0.03243929594882452 0.18898699631444485 chrMT 16571 1400 0.08448494357612697 0.3018380599101455 chrX 155270560 6574116 0.04233974553836864 0.216792905904837 chrY 59373566 460488 0.007755774682625598 0.09027049900521295