BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240049.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 = 2,024,882 number of mapped reads = 1,732,806 (85.58%) number of supplementary alignments = 8,214 (0.41%) number of secondary alignments = 0 number of mapped bases = 110,889,958 bp number of sequenced bases = 110,831,277 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 157,328 duplication rate = 7.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3609 >>>>>>> ACTG content number of A's = 30,524,883 bp (27.54%) number of C's = 19,813,285 bp (17.88%) number of T's = 35,738,638 bp (32.25%) number of G's = 24,678,463 bp (22.27%) number of N's = 76,008 bp (0.07%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,015,254 number of insertions = 7,959 mapped reads with insertion percentage = 0.46% number of deletions = 33,493 mapped reads with deletion percentage = 1.91% homopolymer indels = 49.93% >>>>>>> Coverage mean coverageData = 0.0358X std coverageData = 0.3382X There is a 2.49% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 9616874 0.038583149608281214 0.47566281589412124 chr2 243199373 15876278 0.06528091665762642 0.45199203925811854 chr3 198022430 6735454 0.03401359128862321 0.24914941001778296 chr4 191154276 7772466 0.04066069649417625 0.28598849426693157 chr5 180915260 4176175 0.023083597259844196 0.20508079177006508 chr6 171115067 3791543 0.022157855918088148 0.2189714253401327 chr7 159138663 6286495 0.039503253838446536 0.5235303887225918 chr8 146364022 6656330 0.04547791123149103 0.4545050310872056 chr9 141213431 3887972 0.027532593553370996 0.2978355513582314 chr10 135534747 4949087 0.03651526349918224 0.3267698381957952 chr11 135006516 4766411 0.03530504409135334 0.34047971025573537 chr12 133851895 6663013 0.04977899640494444 0.3083691128766637 chr13 115169878 1759108 0.01527402850943369 0.16495528530820766 chr14 107349540 3980167 0.037076702890389654 0.26805493915111994 chr15 102531392 3679663 0.035888159989089 0.274010246607471 chr16 90354753 3337053 0.0369327886934736 0.26287625116700447 chr17 81195210 1844035 0.022711130373331136 0.2258506979623153 chr18 78077248 2200534 0.028184062020218746 0.4615184046326917 chr19 59128983 1732327 0.029297425934080416 0.3253217875380798 chr20 63025520 2056809 0.032634542325077204 0.247401631563722 chr21 48129895 2112882 0.043899576344390526 0.2946574152207245 chr22 51304566 744134 0.014504245099744144 0.15384828663308475 chrMT 16571 19842 1.1973930360267937 1.6083011921713077 chrX 155270560 6000563 0.03864585147371143 0.2876440058204908 chrY 59373566 244743 0.00412208692332881 0.09359939592893775