BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716924.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 = 2,811,748 number of mapped reads = 2,577,607 (91.67%) number of supplementary alignments = 13,769 (0.49%) number of secondary alignments = 0 number of mapped bases = 149,823,394 bp number of sequenced bases = 149,782,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,254 duplication rate = 3.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6235 >>>>>>> ACTG content number of A's = 38,404,212 bp (25.64%) number of C's = 29,542,781 bp (19.72%) number of T's = 46,593,492 bp (31.11%) number of G's = 35,237,650 bp (23.53%) number of N's = 4,182 bp (0%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 745,329 number of insertions = 8,332 mapped reads with insertion percentage = 0.32% number of deletions = 26,224 mapped reads with deletion percentage = 1.01% homopolymer indels = 43.92% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.4195X There is a 4.12% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 14978998 0.060096131114553974 0.7429086988431438 chr2 243199373 13490148 0.055469501559940286 0.5236420823584428 chr3 198022430 10920841 0.05514951513320991 0.27110713923268526 chr4 191154276 7451557 0.038981900671685735 0.24458886775152314 chr5 180915260 6853055 0.03787991681851492 0.22630747165591333 chr6 171115067 11457812 0.0669596909312492 0.38435797084049556 chr7 159138663 9249946 0.0581250704613498 0.7911762692951113 chr8 146364022 9536755 0.06515778173955893 0.3806194264819504 chr9 141213431 5821520 0.04122497384827368 0.3173702499874372 chr10 135534747 7635849 0.05633868191748644 0.3858615905496567 chr11 135006516 5226594 0.038713642532631536 0.34626479882142125 chr12 133851895 6404388 0.0478468235358192 0.2562785027906551 chr13 115169878 4537295 0.03939654255776845 0.22986417920537872 chr14 107349540 3428556 0.03193824584623278 0.23312562857912128 chr15 102531392 4750415 0.0463313226060561 0.2552470750149309 chr16 90354753 3309151 0.03662398368794168 0.24759516656030162 chr17 81195210 4442349 0.05471195899364014 0.2841483964842861 chr18 78077248 3118303 0.03993868994972773 0.6257928320723491 chr19 59128983 2980001 0.050398313125054085 0.48867083301015013 chr20 63025520 2399032 0.03806445389105873 0.22813003123893089 chr21 48129895 1550278 0.03221029258426598 0.23257389754968527 chr22 51304566 2489677 0.04852739617756439 0.25253131279821295 chrMT 16571 42097 2.540401906945869 2.245021615137956 chrX 155270560 7378682 0.04752144901132578 0.29575352706417496 chrY 59373566 370095 0.006233329492117755 0.13370840986248442