BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819100.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,414,113 number of mapped reads = 1,287,245 (91.03%) number of supplementary alignments = 5,014 (0.35%) number of secondary alignments = 0 number of mapped bases = 74,804,623 bp number of sequenced bases = 74,779,963 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,243 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0455 >>>>>>> ACTG content number of A's = 19,074,966 bp (25.51%) number of C's = 13,339,681 bp (17.84%) number of T's = 23,424,772 bp (31.32%) number of G's = 18,939,402 bp (25.33%) number of N's = 1,142 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 386,683 number of insertions = 4,680 mapped reads with insertion percentage = 0.36% number of deletions = 14,695 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.2363X There is a 2.17% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7057471 0.02831475793996116 0.4306604617263701 chr2 243199373 5917369 0.024331349735839985 0.26246272525404657 chr3 198022430 4398951 0.022214407731487792 0.16451369550803058 chr4 191154276 4189389 0.021916271441398464 0.1802287458644371 chr5 180915260 4091843 0.02261745637156313 0.16430889098183338 chr6 171115067 3198298 0.018690919835831873 0.18176800252721106 chr7 159138663 3770366 0.023692331762269488 0.28456457115690625 chr8 146364022 6846171 0.046774958124613436 0.2737853019694195 chr9 141213431 3168346 0.02243657687206821 0.1999748944621782 chr10 135534747 3904403 0.02880739505124837 0.24760729877795096 chr11 135006516 2580297 0.019112388619820394 0.20520601288821044 chr12 133851895 3475933 0.02596850048331404 0.17600339332913542 chr13 115169878 1636161 0.0142065011130775 0.13095370294962752 chr14 107349540 1760237 0.016397247719925023 0.1421107421519784 chr15 102531392 1976371 0.01927576483112606 0.15378150831578147 chr16 90354753 2329340 0.02577993877090229 0.18457019008997255 chr17 81195210 2623296 0.03230850686881652 0.20610059982833367 chr18 78077248 1784145 0.022851023130323445 0.3460470948909574 chr19 59128983 1555022 0.02629881187031409 0.29495769846667913 chr20 63025520 2138478 0.03393035075315523 0.20208347187284284 chr21 48129895 1022040 0.021235034898787957 0.1761344248957477 chr22 51304566 619195 0.01206900376079587 0.1187836201039346 chrMT 16571 4052 0.2445235652646189 0.5100635025472086 chrX 155270560 4505323 0.02901595125309009 0.20442672126949374 chrY 59373566 252126 0.004246435189693676 0.13256389208256494