BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549105.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 13,335,318 number of mapped reads = 10,646,198 (79.83%) number of secondary alignments = 0 number of mapped bases = 421,833,548 bp number of sequenced bases = 421,790,728 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 496,727 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2295 >>>>>>> ACTG content number of A's = 126,751,830 bp (30.05%) number of C's = 83,802,472 bp (19.87%) number of T's = 127,075,189 bp (30.13%) number of G's = 84,159,511 bp (19.95%) number of N's = 1,726 bp (0%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 1,404,249 number of insertions = 13,138 mapped reads with insertion percentage = 0.12% number of deletions = 34,608 mapped reads with deletion percentage = 0.32% homopolymer indels = 44.22% >>>>>>> Coverage mean coverageData = 0.1363X std coverageData = 1.2243X There is a 9.94% of reference with a coverageData >= 1X There is a 2.45% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.08% 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 0.01% 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% 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 33232220 0.133328534415166 1.1947088327630164 chr2 243199373 37356573 0.1536047257819205 0.7762143945811542 chr3 198022430 30538536 0.1542175601016511 0.5130987192141709 chr4 191154276 30196801 0.1579708371263429 0.5511273355446458 chr5 180915260 28102731 0.15533643209533568 0.5171632256585632 chr6 171115067 25450337 0.14873229719741746 0.5538064114377031 chr7 159138663 23574368 0.14813727572915453 1.0545531280027995 chr8 146364022 22718468 0.15521893761569355 4.60172920302352 chr9 141213431 17724393 0.12551492357692237 0.7339606963983916 chr10 135534747 19489368 0.1437960997558803 0.6980237444722796 chr11 135006516 19687398 0.14582553926508257 0.6767537215327944 chr12 133851895 19065463 0.1424370047207774 0.5055309026640907 chr13 115169878 14625622 0.12699172955622998 0.4638671090832501 chr14 107349540 13095696 0.12199117015312781 0.5975874195128357 chr15 102531392 11788931 0.11497874719188442 0.44016528761256424 chr16 90354753 10769220 0.11918819588826722 0.5147366986178806 chr17 81195210 9604949 0.11829452747274131 0.4660979670492428 chr18 78077248 11723719 0.1501553820134644 1.2984415783686625 chr19 59128983 6545706 0.11070215768804953 1.0705323770904447 chr20 63025520 8205306 0.13019021501131606 0.5012144487584671 chr21 48129895 5560840 0.11553817019546792 0.542474224264679 chr22 51304566 3915605 0.0763207898493869 0.42419984680202627 chrMT 16571 47404 2.860660189487659 3.2040126968570237 chrX 155270560 15500014 0.09982583948946921 0.49080481457759756 chrY 59373566 3313880 0.055814063787241616 0.41358252881743296