BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472499.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,332,836 number of mapped reads = 15,115,908 (98.59%) number of supplementary alignments = 62,262 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,581,736 number of mapped paired reads (second in pair) = 7,534,172 number of mapped paired reads (both in pair) = 15,014,850 number of mapped paired reads (singletons) = 101,058 number of mapped bases = 1,487,403,207 bp number of sequenced bases = 1,487,219,313 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,620,495 duplication rate = 45.53% >>>>>>> Insert size mean insert size = 30,620.3624 std insert size = 1,715,464.8331 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 55.0217 >>>>>>> ACTG content number of A's = 402,898,840 bp (27.09%) number of C's = 343,337,340 bp (23.09%) number of T's = 400,726,683 bp (26.94%) number of G's = 340,027,420 bp (22.86%) number of N's = 229,030 bp (0.02%) GC percentage = 45.95% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 9,092,349 number of insertions = 72,991 mapped reads with insertion percentage = 0.48% number of deletions = 70,145 mapped reads with deletion percentage = 0.46% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 0.4805X std coverageData = 20.1017X There is a 4.75% of reference with a coverageData >= 1X There is a 2.14% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 118087949 0.4737719349553797 16.902637289464955 chr2 243199373 97229372 0.3997928563738526 18.093339800263 chr3 198022430 173881309 0.8780889568924086 26.755163146722754 chr4 191154276 39299924 0.20559270146800168 7.846079565575202 chr5 180915260 74778363 0.41333364029104014 17.058858605417768 chr6 171115067 50145018 0.29304852506062484 8.435991427900086 chr7 159138663 54653956 0.3434360636798865 12.810699946510171 chr8 146364022 72051100 0.4922732992401644 18.538402462809618 chr9 141213431 137895439 0.9765037080644262 30.29352819414167 chr10 135534747 46043399 0.33971656729473215 15.682868344773624 chr11 135006516 68051258 0.504059063341802 17.093337827071686 chr12 133851895 97737016 0.7301877646184987 21.702946043496613 chr13 115169878 32733943 0.28422312820371315 9.603678360691042 chr14 107349540 23227007 0.21636801610887202 7.799020957433229 chr15 102531392 49615744 0.4839078357582427 17.230736483123753 chr16 90354753 41384209 0.458019170280948 17.07185688342159 chr17 81195210 93114214 1.1467944229715028 32.20345226860499 chr18 78077248 22446757 0.28749421342309606 8.951610440731082 chr19 59128983 71872300 1.2155172701008574 71.50004590965716 chr20 63025520 49702402 0.7886075672203895 22.611468065084768 chr21 48129895 5990496 0.12446517907425313 4.580162385768134 chr22 51304566 8907978 0.1736293412948859 6.427449180393659 chrMT 16571 1889 0.11399432743950275 0.4293620165338671 chrX 155270560 57004071 0.36712736142640306 15.560785419862478 chrY 59373566 1548094 0.02607379182850496 0.9349643993014242