BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549038.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 = 7,369,374 number of mapped reads = 6,194,334 (84.06%) number of secondary alignments = 0 number of mapped bases = 245,555,734 bp number of sequenced bases = 245,533,529 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 294,439 duplication rate = 4.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1272 >>>>>>> ACTG content number of A's = 69,882,645 bp (28.46%) number of C's = 51,856,261 bp (21.12%) number of T's = 71,137,829 bp (28.97%) number of G's = 52,656,589 bp (21.45%) number of N's = 205 bp (0%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 597,437 number of insertions = 6,508 mapped reads with insertion percentage = 0.11% number of deletions = 16,853 mapped reads with deletion percentage = 0.27% homopolymer indels = 42.32% >>>>>>> Coverage mean coverageData = 0.0793X std coverageData = 0.4968X There is a 5.72% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.16% 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 0.02% 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 19681075 0.07896098682137286 0.5325820781820688 chr2 243199373 21044850 0.08653332342267182 0.46556543368453823 chr3 198022430 17225361 0.08698691860310975 0.395121723716401 chr4 191154276 16602989 0.08685648758388224 0.401072534153153 chr5 180915260 16039234 0.08865605919589094 0.40035656765778777 chr6 171115067 14905149 0.08710599984745937 0.41257374523596424 chr7 159138663 13646813 0.0857542268028229 0.5331518290208482 chr8 146364022 12844587 0.087757816603318 1.1922362757025773 chr9 141213431 10640000 0.07534694061785101 0.4388742508215582 chr10 135534747 11329241 0.08358919945451332 0.4275465984607938 chr11 135006516 11561270 0.08563490372568387 0.43524305894993753 chr12 133851895 11404322 0.08520105001128299 0.3952422881023377 chr13 115169878 8331701 0.07234270926292029 0.363051728299544 chr14 107349540 7838755 0.07302085318670205 0.3964343172576561 chr15 102531392 6779603 0.06612221747657537 0.3441728778297274 chr16 90354753 6673346 0.07385716609728323 0.37768087062470296 chr17 81195210 6182667 0.07614571105857107 0.3715287054978937 chr18 78077248 6565929 0.08409529239555165 0.6473143943193083 chr19 59128983 4520573 0.07645274399527555 0.5329019696647199 chr20 63025520 5227000 0.08293465884930422 0.40108037047097395 chr21 48129895 3201941 0.06652707220740872 0.3986908444764317 chr22 51304566 2696531 0.05255927903181171 0.4448718596025248 chrMT 16571 16931 1.0217246997767184 1.682662515590156 chrX 155270560 8697672 0.05601623385656624 0.3456363868823465 chrY 59373566 1898194 0.03197035529245456 0.2703027238970656