BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234138.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 = 2,011,542 number of mapped reads = 1,146,673 (57%) number of supplementary alignments = 9,361 (0.47%) number of secondary alignments = 0 number of mapped bases = 71,508,625 bp number of sequenced bases = 71,466,340 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,966 duplication rate = 12.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1207 >>>>>>> ACTG content number of A's = 19,429,016 bp (27.19%) number of C's = 11,559,669 bp (16.17%) number of T's = 24,693,348 bp (34.55%) number of G's = 15,770,607 bp (22.07%) number of N's = 13,700 bp (0.02%) GC percentage = 38.24% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 651,313 number of insertions = 6,343 mapped reads with insertion percentage = 0.55% number of deletions = 24,162 mapped reads with deletion percentage = 2.08% homopolymer indels = 44.26% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.3696X There is a 1.37% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.05% 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 5538198 0.022219394991998837 0.3252101391718713 chr2 243199373 6019180 0.024749981571704133 0.37932810224081376 chr3 198022430 5381404 0.027175729537305446 0.26616843457425043 chr4 191154276 4914000 0.025706984446426925 0.2759055276446277 chr5 180915260 4500409 0.02487578438656861 0.2526612461200118 chr6 171115067 4088037 0.02389057300255155 0.2688584333831758 chr7 159138663 4122940 0.02590784616557951 0.3089463369705426 chr8 146364022 3915135 0.026749299086629364 1.1427324905298502 chr9 141213431 2990202 0.02117505380915219 0.2648753015627048 chr10 135534747 3572480 0.026358406822421708 0.28763209221267316 chr11 135006516 3405825 0.02522711570454866 0.2911821264941217 chr12 133851895 3146949 0.02351067947151589 0.24581801361908875 chr13 115169878 2640466 0.02292670658208043 0.2546549193234808 chr14 107349540 2425356 0.022593073058347526 0.2454113681816198 chr15 102531392 2049897 0.019992872036692918 0.22400643978504722 chr16 90354753 1747014 0.019335053685554316 0.21882011417130903 chr17 81195210 1651996 0.02034597853740387 0.22267884245070088 chr18 78077248 1857977 0.023796650722115616 0.42799651988190035 chr19 59128983 1227448 0.02075882143956374 0.25023954036155505 chr20 63025520 1348566 0.02139714198312049 0.2308841345917646 chr21 48129895 1004121 0.020862729910381062 0.2349974766910114 chr22 51304566 641169 0.012497308719071905 0.1669251333960931 chrMT 16571 16477 0.9943274395027457 1.5864908686922228 chrX 155270560 2718158 0.017505945750437173 0.21343796700850298 chrY 59373566 585221 0.009856591736464002 0.1885951717507133