BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081167.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,524,152 number of mapped reads = 2,245,749 (88.97%) number of supplementary alignments = 19,973 (0.79%) number of secondary alignments = 0 number of mapped bases = 149,783,986 bp number of sequenced bases = 149,730,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,330 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5184 >>>>>>> ACTG content number of A's = 41,731,547 bp (27.87%) number of C's = 27,495,239 bp (18.36%) number of T's = 47,292,522 bp (31.59%) number of G's = 33,166,368 bp (22.15%) number of N's = 44,362 bp (0.03%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,235,217 number of insertions = 11,507 mapped reads with insertion percentage = 0.51% number of deletions = 33,511 mapped reads with deletion percentage = 1.48% homopolymer indels = 46.95% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.3617X There is a 4.16% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11137013 0.044681986970856936 0.5221855602933565 chr2 243199373 11788760 0.04847364470795737 0.4820075222141767 chr3 198022430 8715471 0.044012544437516496 0.23609884963074534 chr4 191154276 10710501 0.056030663943923496 0.27404509521281767 chr5 180915260 9909108 0.05477209606309606 0.26414984760219773 chr6 171115067 10133932 0.059222908757649025 0.38185432500927025 chr7 159138663 8121807 0.051036038929144455 0.4130279264150263 chr8 146364022 8314687 0.056808270819450425 0.487129092606218 chr9 141213431 5484715 0.03883989618522901 0.3379861977985483 chr10 135534747 7459532 0.05503778304171697 0.3321333986842077 chr11 135006516 6724992 0.04981235127940047 0.36028745736517404 chr12 133851895 7266541 0.05428792024199583 0.2659991119107505 chr13 115169878 5018049 0.04357084584217411 0.23487431334266012 chr14 107349540 4434393 0.04130798324799529 0.24227831405732203 chr15 102531392 4521096 0.04409474905012506 0.24307901418182604 chr16 90354753 3966625 0.04390056824127448 0.25931478358821314 chr17 81195210 3905847 0.04810440172517566 0.27524501696044573 chr18 78077248 3846394 0.04926395459020277 0.6453860528816562 chr19 59128983 2257347 0.038176658644712355 0.4163468288131025 chr20 63025520 3057872 0.04851799715416866 0.25172568623388664 chr21 48129895 1944055 0.04039183962483193 0.24329765534602335 chr22 51304566 1674331 0.03263512647197912 0.20185965243178638 chrMT 16571 21797 1.3153702250920283 1.4146329519182983 chrX 155270560 9010278 0.058029532449680093 0.29976517427968674 chrY 59373566 358843 0.0060438175466839906 0.11326293096916827