BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054598.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 3,137,266 number of mapped reads = 2,481,784 (79.11%) number of supplementary alignments = 78 (0%) number of secondary alignments = 0 number of mapped bases = 116,282,229 bp number of sequenced bases = 116,258,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 301,688 duplication rate = 10.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5484 >>>>>>> ACTG content number of A's = 35,279,976 bp (30.35%) number of C's = 22,983,835 bp (19.77%) number of T's = 34,394,719 bp (29.58%) number of G's = 23,586,782 bp (20.29%) number of N's = 13,468 bp (0.01%) GC percentage = 40.06% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 847,232 number of insertions = 5,091 mapped reads with insertion percentage = 0.2% number of deletions = 16,236 mapped reads with deletion percentage = 0.65% homopolymer indels = 44.63% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.3348X There is a 2.42% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 10749621 0.04312776015109707 0.37264589625253086 chr2 243199373 9598254 0.03946660668405588 0.40238461262433944 chr3 198022430 7391072 0.03732441824898321 0.31449070506615545 chr4 191154276 7144540 0.0373757791324532 0.3203236638141177 chr5 180915260 5841813 0.03229032752682112 0.2801046443250308 chr6 171115067 5955736 0.03480544468944982 0.3153872316222129 chr7 159138663 7856464 0.049368669133534195 0.39939571411310276 chr8 146364022 5373879 0.036715846739986416 0.3297430055978615 chr9 141213431 5691219 0.04030225000340088 0.3437577881275 chr10 135534747 4968504 0.03665852565467954 0.3199514012872474 chr11 135006516 5090563 0.037706054128528135 0.34304718780248444 chr12 133851895 4310040 0.03220006709654727 0.2818757100340083 chr13 115169878 3807733 0.033061882725967634 0.2863537517792721 chr14 107349540 2658797 0.02476766085816483 0.2812149589626223 chr15 102531392 3100023 0.03023486699566119 0.2694741520237411 chr16 90354753 3256679 0.036043250541562544 0.31592476507000117 chr17 81195210 2206165 0.027171122532967155 0.2536212972670723 chr18 78077248 4455624 0.05706686793059099 0.4279075567141934 chr19 59128983 2126259 0.03595967480110388 0.3434172174143871 chr20 63025520 2511804 0.03985376082577343 0.3203353263482657 chr21 48129895 1341746 0.0278776008133822 0.294486632746421 chr22 51304566 1448395 0.02823130791126856 0.2605293773566212 chrMT 16571 10986 0.6629654215195221 1.4579369322321172 chrX 155270560 9069322 0.05840979771052542 0.4243964367423303 chrY 59373566 316991 0.005338924732935866 0.12384744599050264