BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231791.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 = 4,944,578 number of mapped reads = 4,244,107 (85.83%) number of supplementary alignments = 22,097 (0.45%) number of secondary alignments = 0 number of mapped bases = 266,121,737 bp number of sequenced bases = 266,004,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 382,820 duplication rate = 6.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2241 >>>>>>> ACTG content number of A's = 64,463,941 bp (24.23%) number of C's = 48,813,530 bp (18.35%) number of T's = 85,460,086 bp (32.13%) number of G's = 67,170,721 bp (25.25%) number of N's = 96,088 bp (0.04%) GC percentage = 43.6% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,046,987 number of insertions = 21,168 mapped reads with insertion percentage = 0.49% number of deletions = 71,072 mapped reads with deletion percentage = 1.66% homopolymer indels = 42% >>>>>>> Coverage mean coverageData = 0.086X std coverageData = 1.2155X There is a 6.72% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 24592308 0.09866498186177036 2.1262721660807915 chr2 243199373 14529952 0.05974502245118864 2.3143628625828785 chr3 198022430 23699964 0.11968322982401539 0.4769247060764007 chr4 191154276 12902733 0.06749905505645085 0.3897553090624085 chr5 180915260 17760659 0.09817114929940128 0.41989088294882054 chr6 171115067 12966182 0.07577463649066041 0.7290974793458432 chr7 159138663 18025405 0.11326854618603903 1.9926703697151822 chr8 146364022 13565301 0.09268193654858706 0.8655144964373686 chr9 141213431 9792692 0.06934674648617524 0.9215348060910812 chr10 135534747 12102275 0.08929278482365854 1.138448976136455 chr11 135006516 11912031 0.08823300795348278 0.8523041209043144 chr12 133851895 8059596 0.06021278966577201 0.36080511857010683 chr13 115169878 12886530 0.11189149649008051 0.5077677259746013 chr14 107349540 12314908 0.11471784601964759 0.560216738296019 chr15 102531392 6144938 0.059932259575681955 0.4354714293107451 chr16 90354753 6261266 0.06929647630158427 0.5146042877714702 chr17 81195210 7189506 0.08854593762366031 0.4814722942089531 chr18 78077248 6797313 0.08705881897886565 2.3883086085977965 chr19 59128983 9973273 0.1686697875388792 1.41343694314077 chr20 63025520 5881839 0.09332471989124405 0.5059124359038115 chr21 48129895 4611196 0.09580731476767194 0.43621610421302365 chr22 51304566 2733956 0.053288746268704425 0.2893129310279288 chrMT 16571 132009 7.966266368957818 6.077423675518358 chrX 155270560 10540226 0.06788296506433673 0.662498059786514 chrY 59373566 745679 0.012559107532803402 0.27880773451867163