BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238503.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 = 3,599,984 number of mapped reads = 3,121,167 (86.7%) number of supplementary alignments = 29,206 (0.81%) number of secondary alignments = 0 number of mapped bases = 189,422,464 bp number of sequenced bases = 189,304,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,196,852 duplication rate = 21.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9373 >>>>>>> ACTG content number of A's = 45,862,134 bp (24.23%) number of C's = 34,113,341 bp (18.02%) number of T's = 63,041,559 bp (33.3%) number of G's = 46,275,392 bp (24.44%) number of N's = 12,462 bp (0.01%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,182,054 number of insertions = 12,986 mapped reads with insertion percentage = 0.41% number of deletions = 68,716 mapped reads with deletion percentage = 2.18% homopolymer indels = 39.57% >>>>>>> Coverage mean coverageData = 0.0612X std coverageData = 1.1953X There is a 1.85% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 29758185 0.11939061527955029 1.1207221788714294 chr2 243199373 8666883 0.035636946317291696 2.906440750692097 chr3 198022430 12990639 0.06560185631496392 0.7131364072641567 chr4 191154276 7406783 0.0387476710173096 0.5191731976263478 chr5 180915260 13065118 0.07221678259755424 0.7178834729222966 chr6 171115067 8120760 0.047457889842044125 0.9937079346413993 chr7 159138663 6331474 0.039785894141890585 0.701391745322699 chr8 146364022 7147159 0.048831392457908816 0.7065619089948387 chr9 141213431 6622084 0.04689415130774636 0.6019935903862493 chr10 135534747 17212142 0.1269943123883944 1.0415898175748441 chr11 135006516 16400913 0.12148238089485992 0.9450632286916287 chr12 133851895 3680433 0.027496308513226504 0.43373273462136186 chr13 115169878 1448249 0.012574893931901187 0.713495207218452 chr14 107349540 5899777 0.05495856805720826 0.6449049715953937 chr15 102531392 3984460 0.038860878822361056 0.7501453363932828 chr16 90354753 11559375 0.12793322560463422 1.0512139250061727 chr17 81195210 2970289 0.03658207177492367 0.5022920188910353 chr18 78077248 8793452 0.11262502489841855 2.85433933508506 chr19 59128983 2844763 0.04811114373470621 0.7191368199838413 chr20 63025520 4680212 0.07425899857708433 0.7467906879337799 chr21 48129895 3178824 0.06604676781447373 0.721570816475744 chr22 51304566 629415 0.012268206303509126 0.2586885020429965 chrMT 16571 1022527 61.70581135719027 39.135292168207165 chrX 155270560 4598950 0.029618943861605188 0.4416159183786584 chrY 59373566 409598 0.006898659245092336 0.4440244448459457