BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013266.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 = 1,724,462 number of mapped reads = 1,492,028 (86.52%) number of supplementary alignments = 10,094 (0.59%) number of secondary alignments = 0 number of mapped bases = 99,017,112 bp number of sequenced bases = 98,976,938 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,423 duplication rate = 6.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7026 >>>>>>> ACTG content number of A's = 26,854,715 bp (27.13%) number of C's = 17,923,646 bp (18.11%) number of T's = 32,009,408 bp (32.34%) number of G's = 22,168,395 bp (22.4%) number of N's = 20,774 bp (0.02%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 775,597 number of insertions = 6,788 mapped reads with insertion percentage = 0.45% number of deletions = 23,872 mapped reads with deletion percentage = 1.58% homopolymer indels = 46.37% >>>>>>> Coverage mean coverageData = 0.032X std coverageData = 0.3882X There is a 2.33% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 11106010 0.044557602125292195 0.4583459297554424 chr2 243199373 17938528 0.07376058490085005 0.5963469981152619 chr3 198022430 6860481 0.034644969259290476 0.2443993894543324 chr4 191154276 4512899 0.023608674074337737 0.19886869745655386 chr5 180915260 3067231 0.016953965077351685 0.16658250301876096 chr6 171115067 9616950 0.0562016552288759 0.36013979004244523 chr7 159138663 8646631 0.05433394272012955 1.1185038637839329 chr8 146364022 5668532 0.038728998578626106 0.3150905353641832 chr9 141213431 2405089 0.017031588163876565 0.1930703449787298 chr10 135534747 3214922 0.02372027890382973 0.25967436578166403 chr11 135006516 5819783 0.04310742305208439 0.28420361228103436 chr12 133851895 3740295 0.027943534157659853 0.21869069019474494 chr13 115169878 1463315 0.012705709386963143 0.15105607116490874 chr14 107349540 1623461 0.01512312954484947 0.1617649940058049 chr15 102531392 1372348 0.0133846617434005 0.1490902701810417 chr16 90354753 1852595 0.020503569967149377 0.18759837142107857 chr17 81195210 1752350 0.021581938146351246 0.1972820326796244 chr18 78077248 1039540 0.013314250010451188 0.22745613997556852 chr19 59128983 836715 0.014150674636159394 0.3022690003496509 chr20 63025520 1043478 0.01655643618648446 0.16722331758642514 chr21 48129895 218001 0.004529430201333288 0.08171312155843453 chr22 51304566 583705 0.011377252465209433 0.13246547845973572 chrMT 16571 38249 2.3081890048880576 2.2882463806182396 chrX 155270560 4450075 0.028660133640272825 0.2242728814836928 chrY 59373566 145929 0.0024578109389622985 0.06326772729382907