BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038442.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 13,107,382 number of mapped reads = 12,439,134 (94.9%) number of supplementary alignments = 215,005 (1.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,291,199 number of mapped paired reads (second in pair) = 6,147,935 number of mapped paired reads (both in pair) = 12,274,938 number of mapped paired reads (singletons) = 164,196 number of mapped bases = 1,784,623,351 bp number of sequenced bases = 1,783,400,731 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,727,770 duplication rate = 7.86% >>>>>>> Insert size mean insert size = 96,993.2611 std insert size = 2,932,558.9799 median insert size = 273 >>>>>>> Mapping quality mean mapping quality = 53.6912 >>>>>>> ACTG content number of A's = 520,938,929 bp (29.21%) number of C's = 364,192,265 bp (20.42%) number of T's = 522,684,200 bp (29.31%) number of G's = 375,547,822 bp (21.06%) number of N's = 37,515 bp (0%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0148 number of mismatches = 25,525,081 number of insertions = 314,248 mapped reads with insertion percentage = 2.38% number of deletions = 623,027 mapped reads with deletion percentage = 4.82% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.5765X std coverageData = 9.2235X There is a 25.61% of reference with a coverageData >= 1X There is a 12.76% of reference with a coverageData >= 2X There is a 6.39% of reference with a coverageData >= 3X There is a 3.52% of reference with a coverageData >= 4X There is a 1.95% of reference with a coverageData >= 5X There is a 1.13% of reference with a coverageData >= 6X There is a 0.67% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 108221055 0.4341856985784601 11.222156026333698 chr2 243199373 158982506 0.6537126475239721 11.818795289897222 chr3 198022430 117701663 0.5943855097627072 1.315094363460802 chr4 191154276 111711040 0.5844025168445617 7.312541430647684 chr5 180915260 121711167 0.672752353781544 1.5726542808692645 chr6 171115067 131348814 0.7676051928261817 15.538841526605422 chr7 159138663 127452928 0.8008922885069105 10.686929746543322 chr8 146364022 80203576 0.5479732990666244 2.7193547416658634 chr9 141213431 73673233 0.5217154804488817 15.631944226735916 chr10 135534747 74962277 0.5530853058662514 17.695419956634602 chr11 135006516 77239958 0.5721202227009546 5.3125679975412705 chr12 133851895 60781997 0.45409889041914575 1.1702336166656357 chr13 115169878 120618475 1.0473092191692692 1.9418730649923337 chr14 107349540 32432936 0.3021245922432458 1.0591873622329449 chr15 102531392 39040567 0.38076696549677197 1.0005711028707047 chr16 90354753 63150598 0.6989183845148689 13.350897523071028 chr17 81195210 37861470 0.4663017682939671 5.888574518809127 chr18 78077248 29744553 0.38096313281943545 12.787867284828826 chr19 59128983 20430241 0.3455199119524853 6.493608496608557 chr20 63025520 54300694 0.8615667748556458 2.6866998361063894 chr21 48129895 15618044 0.3244977783558431 3.514782028909892 chr22 51304566 9437469 0.1839498846944734 0.7522344470542226 chrMT 16571 932102 56.2489891979965 33.049488245778235 chrX 155270560 90826479 0.5849562144942351 1.864708844545023 chrY 59373566 26239509 0.44193924616217256 12.212326543567462