BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237838.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 = 1,795,675 number of mapped reads = 1,574,276 (87.67%) number of supplementary alignments = 9,618 (0.54%) number of secondary alignments = 0 number of mapped bases = 102,049,149 bp number of sequenced bases = 102,006,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,653 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6466 >>>>>>> ACTG content number of A's = 28,242,795 bp (27.69%) number of C's = 19,131,277 bp (18.75%) number of T's = 30,395,416 bp (29.8%) number of G's = 24,142,109 bp (23.67%) number of N's = 95,331 bp (0.09%) GC percentage = 42.42% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 825,645 number of insertions = 9,058 mapped reads with insertion percentage = 0.57% number of deletions = 25,024 mapped reads with deletion percentage = 1.57% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.3637X There is a 2.92% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10369487 0.04160265261686148 0.6207005160323089 chr2 243199373 10688330 0.043948838634546974 0.43056761229096646 chr3 198022430 6675049 0.03370855008697752 0.2113104321305322 chr4 191154276 5761860 0.030142459381865987 0.2509761097151019 chr5 180915260 5374477 0.029707151292820737 0.1874898327553381 chr6 171115067 6655203 0.038893144342455825 0.2657969299464861 chr7 159138663 7286501 0.04578711962661142 0.5740062936964426 chr8 146364022 5297808 0.03619610835783127 0.30214810952985327 chr9 141213431 5538848 0.039223237908581086 0.37358390349660736 chr10 135534747 5129922 0.03784949700020468 0.6126866601976143 chr11 135006516 3738408 0.02769057457937808 0.2551261593840902 chr12 133851895 3905201 0.029175537634338312 0.19595723656148595 chr13 115169878 815172 0.007077996557398454 0.08880796833801098 chr14 107349540 2239741 0.020864001839225394 0.23039322466962414 chr15 102531392 1493582 0.014567070346611505 0.13086720791918033 chr16 90354753 2603932 0.0288189819964424 0.2498477616380676 chr17 81195210 1723469 0.02122623982375315 0.1986573330760674 chr18 78077248 2447797 0.031350964111849844 0.590197465283371 chr19 59128983 2036590 0.03444317653831455 0.4570402724153673 chr20 63025520 2275433 0.036103359401080705 0.2217179607754535 chr21 48129895 1035454 0.02151373901813 0.2250295252020197 chr22 51304566 1425900 0.02779284791143151 0.1818064597946279 chrMT 16571 44979 2.7143201979361535 2.503125548290002 chrX 155270560 7146908 0.04602873848075256 0.27118682386110377 chrY 59373566 339098 0.005711262146524937 0.21606836855387376