BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238252.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,432,833 number of mapped reads = 989,273 (69.04%) number of supplementary alignments = 11,570 (0.81%) number of secondary alignments = 0 number of mapped bases = 61,088,092 bp number of sequenced bases = 61,063,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,224 duplication rate = 7.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0423 >>>>>>> ACTG content number of A's = 17,286,826 bp (28.31%) number of C's = 12,200,948 bp (19.98%) number of T's = 18,289,340 bp (29.95%) number of G's = 13,269,631 bp (21.73%) number of N's = 16,839 bp (0.03%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 571,479 number of insertions = 5,051 mapped reads with insertion percentage = 0.51% number of deletions = 15,432 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.12% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.268X There is a 1.31% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 5367956 0.02153637964256065 0.3928060237322993 chr2 243199373 4161808 0.0171127414872077 0.3385544307146095 chr3 198022430 4493131 0.02269001041952672 0.22531037552631492 chr4 191154276 3410591 0.017842085834376 0.21032103899365934 chr5 180915260 4350021 0.02404452228076283 0.2330532508745334 chr6 171115067 4181668 0.02443775450819886 0.2852728755529025 chr7 159138663 3038548 0.019093713260617252 0.23485642683266833 chr8 146364022 2623736 0.017926099352476115 0.2529104261003061 chr9 141213431 2988902 0.0211658478859564 0.2353733987855477 chr10 135534747 2484639 0.018332118183686137 0.23231631846223394 chr11 135006516 2857532 0.021165882097127817 0.23053900082758408 chr12 133851895 3211087 0.023989850872115033 0.23482857921323194 chr13 115169878 2055829 0.017850405294342675 0.2167308664648789 chr14 107349540 1553458 0.01447102614505847 0.3422593107408847 chr15 102531392 2191661 0.02137551199929091 0.37260427055764106 chr16 90354753 1513456 0.016750153696950508 0.19237966125867023 chr17 81195210 1513447 0.018639609405530205 0.20515813169257804 chr18 78077248 1833564 0.023483973205612983 0.2917655363282277 chr19 59128983 1233617 0.020863152677596367 0.281998256487157 chr20 63025520 1266100 0.020088687883892113 0.2107440717490454 chr21 48129895 735319 0.015277801873451001 0.1779694673191615 chr22 51304566 733961 0.014305958654830059 0.1749719956223636 chrMT 16571 15157 0.9146702069881117 1.5133854330362702 chrX 155270560 3102419 0.019980729122120768 0.24378646195246462 chrY 59373566 170485 0.0028713956645285547 0.08599101501800425