BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237827.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 = 1,546,120 number of mapped reads = 1,304,987 (84.4%) number of supplementary alignments = 15,504 (1%) number of secondary alignments = 0 number of mapped bases = 84,251,486 bp number of sequenced bases = 84,199,251 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 209,378 duplication rate = 11.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2764 >>>>>>> ACTG content number of A's = 22,831,352 bp (27.12%) number of C's = 15,417,515 bp (18.31%) number of T's = 26,777,038 bp (31.8%) number of G's = 19,040,003 bp (22.61%) number of N's = 133,343 bp (0.16%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 775,527 number of insertions = 5,747 mapped reads with insertion percentage = 0.44% number of deletions = 30,060 mapped reads with deletion percentage = 2.27% homopolymer indels = 43.6% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.3552X There is a 1.36% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 5980246 0.023992903110961555 0.5717803806330504 chr2 243199373 6935379 0.028517256909210864 0.39089355761001976 chr3 198022430 5587525 0.02821662677303778 0.3044127556788473 chr4 191154276 5245377 0.027440542318812686 0.3051695170688264 chr5 180915260 6445927 0.03562953727618112 0.3395496962841753 chr6 171115067 4813613 0.028130854192985822 0.31585475930250345 chr7 159138663 5539072 0.03480657619952481 0.40617039856655435 chr8 146364022 2837827 0.01938882903887405 0.3182481706906365 chr9 141213431 3030500 0.02146042326526292 0.2887719153990753 chr10 135534747 4046278 0.029854174590372755 0.36957826561903706 chr11 135006516 3346023 0.02478415930679968 0.29544722016309 chr12 133851895 5503159 0.041113792225354745 0.378780635012382 chr13 115169878 2744775 0.023832403469247403 0.2857415334955231 chr14 107349540 2344743 0.021842133650502835 0.2701383520860277 chr15 102531392 2032246 0.019820719882550703 0.25058297432745996 chr16 90354753 2516851 0.027855214213246757 0.3124933682247778 chr17 81195210 2547019 0.03136907953067675 0.34300335147593314 chr18 78077248 2037002 0.02608957221443051 0.3847520516023153 chr19 59128983 1814946 0.030694693328312445 0.4588599924861145 chr20 63025520 1933419 0.030676763952126058 0.3189270728995504 chr21 48129895 1494075 0.031042556814221182 0.324944308614357 chr22 51304566 1192524 0.023244013018256505 0.281191644944161 chrMT 16571 26738 1.6135417295274879 1.9804465777259528 chrX 155270560 4037679 0.026004150432638356 0.28897048308473117 chrY 59373566 218543 0.0036808131079746837 0.10918265071766264