BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236109.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 = 257,336 number of mapped reads = 217,897 (84.67%) number of supplementary alignments = 1,566 (0.61%) number of secondary alignments = 0 number of mapped bases = 13,703,032 bp number of sequenced bases = 13,697,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,726 duplication rate = 0.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9318 >>>>>>> ACTG content number of A's = 3,908,972 bp (28.54%) number of C's = 2,612,124 bp (19.07%) number of T's = 4,174,955 bp (30.48%) number of G's = 2,995,265 bp (21.87%) number of N's = 5,940 bp (0.04%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 157,454 number of insertions = 1,132 mapped reads with insertion percentage = 0.51% number of deletions = 3,431 mapped reads with deletion percentage = 1.56% homopolymer indels = 44.6% >>>>>>> Coverage mean coverageData = 0.0044X std coverageData = 0.0768X There is a 0.43% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% 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 1169225 0.00469096123134634 0.10807512046643757 chr2 243199373 939467 0.003862949926273042 0.07477495478606616 chr3 198022430 1086504 0.0054867723823003286 0.07555826455074684 chr4 191154276 906025 0.004739757953413503 0.07079473705341424 chr5 180915260 893819 0.004940539565319145 0.07153880743056378 chr6 171115067 793575 0.004637668756544974 0.07150091795072269 chr7 159138663 811309 0.0050981262799725795 0.09180830571492107 chr8 146364022 736589 0.005032582392413349 0.09109784269409535 chr9 141213431 599213 0.004243314504553041 0.07240164863197589 chr10 135534747 580773 0.004285048763178051 0.07023836274948954 chr11 135006516 623472 0.004618088211386775 0.07388893133535898 chr12 133851895 551257 0.004118410127850637 0.06581090031518536 chr13 115169878 395938 0.003437860722575394 0.06073928335890325 chr14 107349540 419823 0.003910803902839267 0.06551174114720226 chr15 102531392 361049 0.003521350807370293 0.060669205435303526 chr16 90354753 344282 0.0038103363527539056 0.0642055550221536 chr17 81195210 349316 0.004302174968203174 0.06787011001209965 chr18 78077248 367450 0.004706236572272629 0.10034326183685868 chr19 59128983 286725 0.004849144792495416 0.08314649330811888 chr20 63025520 271943 0.004314807715985525 0.06686039513991367 chr21 48129895 169030 0.00351195447237107 0.06101151813207148 chr22 51304566 135998 0.002650797201948848 0.0521948002081153 chrMT 16571 16164 0.9754390199746545 1.207583884176833 chrX 155270560 853454 0.005496560326696832 0.07690215800991002 chrY 59373566 40632 6.843449490636962E-4 0.028943923941064664