BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708546.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,114,104 number of mapped reads = 3,376,532 (82.07%) number of supplementary alignments = 106 (0%) number of secondary alignments = 0 number of mapped bases = 168,373,071 bp number of sequenced bases = 168,357,612 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,750 duplication rate = 0.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5266 >>>>>>> ACTG content number of A's = 52,322,954 bp (31.08%) number of C's = 31,862,624 bp (18.93%) number of T's = 51,944,515 bp (30.85%) number of G's = 32,221,532 bp (19.14%) number of N's = 5,987 bp (0%) GC percentage = 38.06% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 271,148 number of insertions = 11,341 mapped reads with insertion percentage = 0.34% number of deletions = 9,083 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.2407X There is a 5.14% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 12594287 0.05052860831187257 0.23272714267091904 chr2 243199373 15087606 0.062038013560174764 0.2559862544551254 chr3 198022430 12209935 0.06165935343789085 0.2549529917325933 chr4 191154276 13428695 0.07025056033797539 0.2723828503763659 chr5 180915260 11843089 0.06546207876549497 0.2627931924671278 chr6 171115067 11643075 0.0680423717450901 0.26869123320969 chr7 159138663 9485264 0.05960376831870204 0.2519564844821813 chr8 146364022 9394774 0.0641877277737011 0.2609203813352452 chr9 141213431 7040957 0.049860391820661876 0.23104882889817055 chr10 135534747 7199566 0.05311970663877065 0.23686786849307745 chr11 135006516 7297891 0.05405584275650814 0.24025689556853777 chr12 133851895 8086455 0.06041345174829239 0.2533713274434225 chr13 115169878 5835724 0.050670575512809 0.2319699168030787 chr14 107349540 5539173 0.051599410672835674 0.23518344659625032 chr15 102531392 4257127 0.041520230213981685 0.2102991592304121 chr16 90354753 2993459 0.033130066771362876 0.18752449213335634 chr17 81195210 2676582 0.032964777109388596 0.18711881707813602 chr18 78077248 4760932 0.06097720042591665 0.2536939900517251 chr19 59128983 1359348 0.022989537973281224 0.15506046690829825 chr20 63025520 2343046 0.03717614705915953 0.19860449054890708 chr21 48129895 2037885 0.04234135561691959 0.2134775423629114 chr22 51304566 840622 0.016384935407113665 0.13103851262757174 chrMT 16571 250 0.01508659706716553 0.12189746369838267 chrX 155270560 10169035 0.06549235734063173 0.2636914328744133 chrY 59373566 248294 0.004181894683570126 0.06725868351844203