BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716727.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 = 457,292 number of mapped reads = 390,298 (85.35%) number of supplementary alignments = 1,694 (0.37%) number of secondary alignments = 0 number of mapped bases = 22,591,181 bp number of sequenced bases = 22,584,772 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,722 duplication rate = 0.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.209 >>>>>>> ACTG content number of A's = 6,070,770 bp (26.88%) number of C's = 4,158,660 bp (18.41%) number of T's = 6,937,248 bp (30.72%) number of G's = 5,417,799 bp (23.99%) number of N's = 295 bp (0%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 110,623 number of insertions = 1,878 mapped reads with insertion percentage = 0.48% number of deletions = 4,065 mapped reads with deletion percentage = 1.04% homopolymer indels = 40.03% >>>>>>> Coverage mean coverageData = 0.0073X std coverageData = 0.1003X There is a 0.7% of reference with a coverageData >= 1X There is a 0.02% 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 1885399 0.007564270020414513 0.13426804121230196 chr2 243199373 2284436 0.009393264348588596 0.11951307677495855 chr3 198022430 1550270 0.00782875960061696 0.09071232914164329 chr4 191154276 1309272 0.006849294859613813 0.08536643839966786 chr5 180915260 1227663 0.006785845483681144 0.08414304978214432 chr6 171115067 1289292 0.007534649184340968 0.09107438401793173 chr7 159138663 1117891 0.0070246348619882526 0.14266113646034786 chr8 146364022 1938919 0.01324723776721577 0.12514558675316262 chr9 141213431 924193 0.00654465367391293 0.08690330100349704 chr10 135534747 1062819 0.007841671774397454 0.10566553597854984 chr11 135006516 716947 0.0053104622002096554 0.07999373404453135 chr12 133851895 1040214 0.00777138045001156 0.09093248883906857 chr13 115169878 603727 0.0052420564342353475 0.07377740045033337 chr14 107349540 750023 0.006986736971579012 0.08569710277188139 chr15 102531392 533440 0.005202699286478038 0.07410050365218827 chr16 90354753 597608 0.006614018412512289 0.08390499165788909 chr17 81195210 905328 0.01115001734708242 0.10910321335362354 chr18 78077248 535673 0.006860807901426034 0.11125286528379055 chr19 59128983 418475 0.007077324499222319 0.1118958231781833 chr20 63025520 491996 0.007806298147163244 0.0905695473967496 chr21 48129895 233663 0.004854841258224229 0.07142269597928536 chr22 51304566 314085 0.0061219697287761875 0.07983038130732888 chrMT 16571 14989 0.9045320137589765 1.0785844051248796 chrX 155270560 800498 0.005155504044037711 0.07527143172937958 chrY 59373566 44361 7.471506764474952E-4 0.029973236131105432