BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240014.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 = 1,373,852 number of mapped reads = 1,117,632 (81.35%) number of supplementary alignments = 5,811 (0.42%) number of secondary alignments = 0 number of mapped bases = 69,708,985 bp number of sequenced bases = 69,671,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,506 duplication rate = 5.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9803 >>>>>>> ACTG content number of A's = 19,212,269 bp (27.58%) number of C's = 12,278,108 bp (17.62%) number of T's = 22,602,886 bp (32.44%) number of G's = 15,532,904 bp (22.29%) number of N's = 45,051 bp (0.06%) GC percentage = 39.92% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 670,008 number of insertions = 4,948 mapped reads with insertion percentage = 0.44% number of deletions = 21,939 mapped reads with deletion percentage = 1.94% homopolymer indels = 48.88% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.2268X There is a 1.78% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 5038633 0.020215127167125493 0.3152811137763255 chr2 243199373 7534433 0.030980478720230912 0.2730551540526136 chr3 198022430 4456786 0.02250647060537536 0.18375944222494384 chr4 191154276 4431094 0.023180721314337745 0.190316550783324 chr5 180915260 3953650 0.021853601514874976 0.18117687126701487 chr6 171115067 3875337 0.022647549791743354 0.2037275140462057 chr7 159138663 4123441 0.025910994363450193 0.3132639213465693 chr8 146364022 4889335 0.033405306394217564 0.3170210918384409 chr9 141213431 2400435 0.016998630958835637 0.1943219935882023 chr10 135534747 3336934 0.024620505618385816 0.21409600573217064 chr11 135006516 3163947 0.023435513290336298 0.21502322259783158 chr12 133851895 3542787 0.026467962967576964 0.20172448104464527 chr13 115169878 1562135 0.013563746242745868 0.1417386651648553 chr14 107349540 2492195 0.02321570264763128 0.19358426126799938 chr15 102531392 1682529 0.016409891323820123 0.1645662283222305 chr16 90354753 1965101 0.021748728592064216 0.18212310725895905 chr17 81195210 1690443 0.020819491691689694 0.18732386133386708 chr18 78077248 1655148 0.021198851680837932 0.3045724225881343 chr19 59128983 1140428 0.01928712354142807 0.22944525625780993 chr20 63025520 1357415 0.021537545426043293 0.18140696707702925 chr21 48129895 1028180 0.021362606338534502 0.18272564653472434 chr22 51304566 632150 0.012321515398843838 0.13292320887343206 chrMT 16571 21218 1.280429666284473 1.793986344959185 chrX 155270560 3591428 0.0231301284673669 0.1946590512358249 chrY 59373566 143803 0.002422003758372876 0.05886322767460757