BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238290.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 = 1,991,894 number of mapped reads = 1,605,277 (80.59%) number of supplementary alignments = 23,027 (1.16%) number of secondary alignments = 0 number of mapped bases = 103,641,543 bp number of sequenced bases = 103,591,288 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,362 duplication rate = 4.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5588 >>>>>>> ACTG content number of A's = 29,011,418 bp (28.01%) number of C's = 19,891,565 bp (19.2%) number of T's = 31,821,103 bp (30.72%) number of G's = 22,841,649 bp (22.05%) number of N's = 25,553 bp (0.02%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 915,986 number of insertions = 8,008 mapped reads with insertion percentage = 0.5% number of deletions = 30,431 mapped reads with deletion percentage = 1.87% homopolymer indels = 45% >>>>>>> Coverage mean coverageData = 0.0335X std coverageData = 0.3299X There is a 2.53% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 3367130 0.013509013484062693 0.45791305066340043 chr2 243199373 9829977 0.04041941752867924 0.45036187880997824 chr3 198022430 8895603 0.044922198965036436 0.26733656688639335 chr4 191154276 5427807 0.02839490234578901 0.23253250298734615 chr5 180915260 5221144 0.02885961084764215 0.2171645020913401 chr6 171115067 6108672 0.035699205844918376 0.2839203946613456 chr7 159138663 4844152 0.030439818386560152 0.3468419251362279 chr8 146364022 2150657 0.014693891098455876 0.36853709170244553 chr9 141213431 4540301 0.03215204791674526 0.35262187609437984 chr10 135534747 1975865 0.014578291130022916 0.252171761654243 chr11 135006516 5289372 0.03917864231086446 0.3191504283782596 chr12 133851895 5202950 0.03887094762461152 0.25394896967378927 chr13 115169878 4056286 0.03522002515275739 0.2375076147396953 chr14 107349540 4913745 0.04577332143202477 0.2987001659559979 chr15 102531392 4753822 0.04636455145366601 0.2778393203440231 chr16 90354753 3141788 0.03477169596158378 0.2576952035478457 chr17 81195210 1555990 0.019163568885405925 0.1929669882019869 chr18 78077248 3874306 0.04962144669853118 0.5907978770728999 chr19 59128983 2104305 0.03558838480276246 0.35607754492468097 chr20 63025520 3127821 0.049627849163323044 0.28596102754997993 chr21 48129895 798898 0.016598789588051253 0.18912706715812366 chr22 51304566 1091185 0.02126876972314706 0.18167607271616415 chrMT 16571 71405 4.309033854323819 3.433499076001421 chrX 155270560 10937432 0.0704411190376334 0.3762779344631021 chrY 59373566 360930 0.006078967869303993 0.15421928327302864