BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231861.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 = 838,383 number of mapped reads = 509,015 (60.71%) number of supplementary alignments = 2,625 (0.31%) number of secondary alignments = 0 number of mapped bases = 33,319,380 bp number of sequenced bases = 33,300,990 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,380 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0453 >>>>>>> ACTG content number of A's = 9,346,954 bp (28.07%) number of C's = 5,754,678 bp (17.28%) number of T's = 10,818,585 bp (32.49%) number of G's = 7,379,282 bp (22.16%) number of N's = 1,491 bp (0%) GC percentage = 39.44% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 301,616 number of insertions = 2,819 mapped reads with insertion percentage = 0.55% number of deletions = 10,403 mapped reads with deletion percentage = 2.02% homopolymer indels = 44.34% >>>>>>> Coverage mean coverageData = 0.0108X std coverageData = 0.1349X There is a 1% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4490183 0.018014731445744323 0.2001802310835617 chr2 243199373 3258124 0.013396925986318229 0.15196778019306495 chr3 198022430 3148855 0.015901506713153657 0.13408370742129105 chr4 191154276 1483199 0.007759172491647532 0.09375136190587062 chr5 180915260 1636033 0.009043090118545002 0.10117912244065827 chr6 171115067 2136463 0.012485534076318364 0.1338621189932272 chr7 159138663 2345900 0.014741232305062158 0.16296827890234453 chr8 146364022 777717 0.005313580409808634 0.2361844146906144 chr9 141213431 1091940 0.007732550595700773 0.10199202099147088 chr10 135534747 1248024 0.009208147929770363 0.1104542255507345 chr11 135006516 862101 0.006385625120494184 0.08922114661773442 chr12 133851895 442565 0.003306378292216184 0.06174404588612115 chr13 115169878 2072027 0.01799104970832738 0.14296345003140806 chr14 107349540 2355809 0.0219452174643692 0.1602569425884927 chr15 102531392 766339 0.007474188978142421 0.09240237379969038 chr16 90354753 728820 0.008066205438024937 0.09978945319237441 chr17 81195210 350296 0.004314244645712475 0.07072139870987677 chr18 78077248 725466 0.009291644090734345 0.15554432403420285 chr19 59128983 667304 0.011285565320817374 0.13147917466224385 chr20 63025520 661393 0.010494050663921535 0.1108667136941816 chr21 48129895 552201 0.0114731395113162 0.1145371586003398 chr22 51304566 114028 0.002222570209442957 0.049006098910419654 chrMT 16571 16934 1.0219057389415243 1.1665742421594154 chrX 155270560 1315980 0.00847539932875878 0.09964359866896721 chrY 59373566 71679 0.0012072544202583351 0.040411150140455855