BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716954.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 10,125,133 number of mapped reads = 7,123,361 (70.35%) number of supplementary alignments = 34,252 (0.34%) number of secondary alignments = 0 number of mapped bases = 408,960,597 bp number of sequenced bases = 408,845,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 611,833 duplication rate = 6.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7163 >>>>>>> ACTG content number of A's = 104,826,666 bp (25.64%) number of C's = 78,012,796 bp (19.08%) number of T's = 129,798,304 bp (31.75%) number of G's = 96,201,648 bp (23.53%) number of N's = 5,799 bp (0%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 2,043,087 number of insertions = 25,783 mapped reads with insertion percentage = 0.36% number of deletions = 73,717 mapped reads with deletion percentage = 1.03% homopolymer indels = 41.89% >>>>>>> Coverage mean coverageData = 0.1321X std coverageData = 0.9948X There is a 9.36% of reference with a coverageData >= 1X There is a 2.39% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 46076673 0.1848608152514894 1.9907773929845833 chr2 243199373 33605350 0.13818024933806058 1.372970073397856 chr3 198022430 35657159 0.18006626320058794 0.5953890073938813 chr4 191154276 18375323 0.09612823413900508 0.48569317028665127 chr5 180915260 17672983 0.09768652461931625 0.4417378559685367 chr6 171115067 33977876 0.19856741195093008 1.0305613714798394 chr7 159138663 23132322 0.1453595346594058 1.2834342686264 chr8 146364022 32059735 0.21904109057620733 0.8064621008012743 chr9 141213431 16685257 0.11815630341847583 0.8460290361742352 chr10 135534747 20329222 0.1499926952311351 1.1029465486801004 chr11 135006516 13100655 0.09703720522644996 0.7386634448639535 chr12 133851895 19061888 0.1424102960962936 0.5750022279471951 chr13 115169878 9176237 0.07967566832014877 0.3867141861689986 chr14 107349540 8593605 0.0800525554184955 0.5951429173888044 chr15 102531392 11884585 0.11591167122748124 0.5068293582482061 chr16 90354753 8743080 0.09676391899383534 0.5764417285225049 chr17 81195210 9183081 0.11309880225693117 0.5030584712524833 chr18 78077248 7604318 0.09739480059543082 1.5589051748969334 chr19 59128983 11054732 0.18695961674159017 1.3118094170536891 chr20 63025520 6714577 0.10653743118660504 0.45270787089900966 chr21 48129895 3586015 0.07450701897438172 0.4943410637228275 chr22 51304566 4791360 0.09339051810710182 0.413408494850736 chrMT 16571 378263 22.82680586566894 12.432987720954804 chrX 155270560 16624034 0.10706494521562877 0.6412948433362374 chrY 59373566 892267 0.0150280176871977 0.3062809334988768