BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549018.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,114,381 number of mapped reads = 6,154,989 (86.51%) number of secondary alignments = 0 number of mapped bases = 243,726,320 bp number of sequenced bases = 243,702,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 347,115 duplication rate = 4.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6592 >>>>>>> ACTG content number of A's = 70,453,112 bp (28.91%) number of C's = 51,047,538 bp (20.95%) number of T's = 70,795,334 bp (29.05%) number of G's = 51,403,820 bp (21.09%) number of N's = 2,399 bp (0%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 633,210 number of insertions = 6,871 mapped reads with insertion percentage = 0.11% number of deletions = 18,409 mapped reads with deletion percentage = 0.3% homopolymer indels = 43.95% >>>>>>> Coverage mean coverageData = 0.0787X std coverageData = 0.769X There is a 5.31% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 19101002 0.07663371879823722 0.7849348722744575 chr2 243199373 20765020 0.0853827036799145 0.5248440791406136 chr3 198022430 16068522 0.08114495918467418 0.3969888920831899 chr4 191154276 15816375 0.08274141353761817 0.41431651699636296 chr5 180915260 14451118 0.07987782788472349 0.3943535117045338 chr6 171115067 14315635 0.0836608678065737 0.4417165821498137 chr7 159138663 13665818 0.08587365095558205 0.6690072350101782 chr8 146364022 13028908 0.0890171493100948 2.6887459044906334 chr9 141213431 10024186 0.07098606647408773 0.46984175819168417 chr10 135534747 11313547 0.083473406269759 0.47211144726659576 chr11 135006516 11216899 0.08308413054670635 0.6565775780464039 chr12 133851895 11276858 0.08424877361654087 0.41153098695377116 chr13 115169878 7852180 0.06817911190285363 0.3625605255345531 chr14 107349540 7426290 0.0691785917294103 0.4146898695850225 chr15 102531392 7051775 0.06877674107847867 0.3612360480081557 chr16 90354753 7048989 0.07801458989102654 0.40591676654766534 chr17 81195210 6604405 0.08133983519471161 0.43313357478114395 chr18 78077248 6316257 0.08089753624512995 0.7544600113828898 chr19 59128983 5108127 0.08638956296610073 0.7092537063355708 chr20 63025520 5045237 0.08005070009735739 0.4014110167343312 chr21 48129895 3158438 0.06562320570198626 0.3837684411173452 chr22 51304566 2851441 0.05557869839499276 0.36584341578328083 chrMT 16571 57559 3.473477762355923 4.28023184141827 chrX 155270560 13441501 0.0865682522172909 0.4703151459131393 chrY 59373566 720233 0.012130532971524735 0.19851010257113408