BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082718.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,341,860 number of mapped reads = 3,055,666 (91.44%) number of supplementary alignments = 12,949 (0.39%) number of secondary alignments = 0 number of mapped bases = 200,736,776 bp number of sequenced bases = 200,657,118 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,510 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7352 >>>>>>> ACTG content number of A's = 54,169,357 bp (27%) number of C's = 34,536,054 bp (17.21%) number of T's = 66,765,843 bp (33.27%) number of G's = 45,134,833 bp (22.49%) number of N's = 51,031 bp (0.03%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,853,147 number of insertions = 18,796 mapped reads with insertion percentage = 0.61% number of deletions = 49,696 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.81% >>>>>>> Coverage mean coverageData = 0.0648X std coverageData = 0.6121X There is a 5.37% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15226333 0.06108844559308039 0.7633817088664865 chr2 243199373 21160922 0.08701059438997813 1.019846314982121 chr3 198022430 14567617 0.07356548952560577 0.31512882840187495 chr4 191154276 11640996 0.06089843368191251 0.3030377703022522 chr5 180915260 11412007 0.06307929469299604 0.2945505615242998 chr6 171115067 12130563 0.07089126172623945 0.5704287295583639 chr7 159138663 10466175 0.06576764440958009 0.8378739358144304 chr8 146364022 17442275 0.1191705089929819 0.7184486496631726 chr9 141213431 6011253 0.04256856417574048 0.786205694551826 chr10 135534747 7888834 0.05820525123347152 0.46409733644010137 chr11 135006516 8657118 0.06412370496250715 0.5744640327764793 chr12 133851895 6888624 0.05146452353177368 0.2856363805896635 chr13 115169878 4735448 0.04111707055902239 0.22987553377756959 chr14 107349540 4883893 0.045495239197112534 0.3572374938747069 chr15 102531392 4528669 0.04416860935624477 0.24116506810910168 chr16 90354753 8115400 0.08981707913030319 0.40152496479802874 chr17 81195210 5227780 0.0643853251934443 0.42039213073760834 chr18 78077248 6836708 0.08756338338154541 1.4468817923229202 chr19 59128983 3672518 0.062110285238628236 0.7095933188763897 chr20 63025520 4125033 0.06545020175954122 0.3290857876501179 chr21 48129895 3659559 0.07603505056472698 0.3398478388565513 chr22 51304566 2609181 0.05085670152633198 0.25856547824341264 chrMT 16571 36001 2.172530324060105 2.8417999817015844 chrX 155270560 8439753 0.05435513982818121 0.42264812039611266 chrY 59373566 374116 0.006301053233016188 0.1367582475261116