BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819075.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,050,577 number of mapped reads = 936,405 (89.13%) number of supplementary alignments = 4,002 (0.38%) number of secondary alignments = 0 number of mapped bases = 53,748,807 bp number of sequenced bases = 53,734,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,244 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6467 >>>>>>> ACTG content number of A's = 13,659,753 bp (25.42%) number of C's = 9,915,846 bp (18.45%) number of T's = 16,498,850 bp (30.7%) number of G's = 13,659,121 bp (25.42%) number of N's = 1,181 bp (0%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 255,616 number of insertions = 4,147 mapped reads with insertion percentage = 0.44% number of deletions = 8,358 mapped reads with deletion percentage = 0.89% homopolymer indels = 38.4% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 0.1637X There is a 1.62% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5914856 0.0237305567234675 0.23509815643240015 chr2 243199373 4428255 0.01820833230519883 0.17816893221337382 chr3 198022430 3498643 0.017667912670296996 0.14004088738715434 chr4 191154276 3367406 0.017616168837363597 0.14561918849576036 chr5 180915260 2618980 0.014476280220916687 0.12814768789423406 chr6 171115067 2786271 0.016283025503534415 0.14128251656136245 chr7 159138663 2360462 0.014832737409638789 0.14525927478666587 chr8 146364022 3334647 0.022783242455581058 0.17595189633709368 chr9 141213431 1932431 0.013684470282433686 0.1546255526010131 chr10 135534747 2488859 0.018363254110770576 0.1667430793971248 chr11 135006516 1673096 0.012392705549115866 0.14735248909361254 chr12 133851895 2332621 0.01742688065790925 0.13999364630199068 chr13 115169878 1630464 0.014157035053905328 0.12499578767198469 chr14 107349540 2787166 0.025963464771251 0.17818796795755854 chr15 102531392 1502947 0.014658408226818962 0.1273344880252289 chr16 90354753 1547830 0.01713058747446302 0.14710937205490826 chr17 81195210 1171444 0.014427501326740826 0.12880596495026567 chr18 78077248 1307124 0.016741419984474863 0.2976840271712519 chr19 59128983 993369 0.016800035272042477 0.1727796219919739 chr20 63025520 1693203 0.026865355494091917 0.1758162236951223 chr21 48129895 689934 0.014334832851806555 0.13434093108720754 chr22 51304566 633763 0.01235295509565367 0.11692542892833353 chrMT 16571 1179 0.07114839176875264 0.27543132177912516 chrX 155270560 2905086 0.018709831406546095 0.15671386301980333 chrY 59373566 148771 0.0025056773581697955 0.06564784376921784