BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234148.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 954,227 number of mapped reads = 263,230 (27.59%) number of supplementary alignments = 2,232 (0.23%) number of secondary alignments = 0 number of mapped bases = 16,452,815 bp number of sequenced bases = 16,443,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,134 duplication rate = 7.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.107 >>>>>>> ACTG content number of A's = 4,477,478 bp (27.23%) number of C's = 2,820,658 bp (17.15%) number of T's = 5,447,361 bp (33.13%) number of G's = 3,695,784 bp (22.47%) number of N's = 2,706 bp (0.02%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 148,427 number of insertions = 1,905 mapped reads with insertion percentage = 0.71% number of deletions = 4,950 mapped reads with deletion percentage = 1.85% homopolymer indels = 42.49% >>>>>>> Coverage mean coverageData = 0.0053X std coverageData = 0.1268X There is a 0.37% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 1364360 0.005473847946802107 0.11496183682830272 chr2 243199373 1471385 0.006050118394014116 0.18520448416354857 chr3 198022430 1146426 0.005789374466316771 0.1064538202142811 chr4 191154276 1187327 0.006211354644245572 0.1511203800317685 chr5 180915260 1008057 0.005571984364392478 0.10621119653902854 chr6 171115067 1027544 0.0060049884444132555 0.11256583738380743 chr7 159138663 902563 0.005671550728059089 0.12405229611074602 chr8 146364022 912305 0.006233123328627851 0.15076777439042813 chr9 141213431 683168 0.004837840106016545 0.09723839242005392 chr10 135534747 756193 0.005579329409896637 0.11626234203795376 chr11 135006516 692391 0.005128574683017522 0.10158191091821396 chr12 133851895 738589 0.0055179569926895695 0.10647565960273737 chr13 115169878 530263 0.004604181312061475 0.10878735249735537 chr14 107349540 503174 0.004687248776287257 0.09768008682748706 chr15 102531392 428001 0.004174341064246938 0.0918398201246762 chr16 90354753 428603 0.004743557873485637 0.09554399430712417 chr17 81195210 387652 0.0047743210467711085 0.094513155500843 chr18 78077248 442305 0.0056649665725923126 0.296503163092278 chr19 59128983 300195 0.005076951856249582 0.10112867963228817 chr20 63025520 345825 0.005487063018282118 0.10503016117421031 chr21 48129895 216760 0.004503645810987122 0.09427559672130544 chr22 51304566 157803 0.0030758081064363747 0.07885458994057927 chrMT 16571 5724 0.34542272644982197 0.8027621254021388 chrX 155270560 733414 0.004723458200962243 0.10046142710682449 chrY 59373566 82788 0.0013943578864708918 0.05140592884690266