BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716827.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 = 600,679 number of mapped reads = 505,290 (84.12%) number of supplementary alignments = 707 (0.12%) number of secondary alignments = 0 number of mapped bases = 26,792,346 bp number of sequenced bases = 26,786,152 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,682 duplication rate = 5.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6321 >>>>>>> ACTG content number of A's = 5,302,297 bp (19.79%) number of C's = 4,986,794 bp (18.62%) number of T's = 8,627,176 bp (32.21%) number of G's = 7,869,289 bp (29.38%) number of N's = 596 bp (0%) GC percentage = 48% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 163,362 number of insertions = 1,293 mapped reads with insertion percentage = 0.25% number of deletions = 3,677 mapped reads with deletion percentage = 0.73% homopolymer indels = 41.03% >>>>>>> Coverage mean coverageData = 0.0087X std coverageData = 0.1084X There is a 0.78% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% 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 2671239 0.010717080620633639 0.1226408427245879 chr2 243199373 2334071 0.009597356157657529 0.13413116036364892 chr3 198022430 1779234 0.008985012455407199 0.10563041031487672 chr4 191154276 1667653 0.008724120824793897 0.1041871673978193 chr5 180915260 1661179 0.009182083368755074 0.10526740046939172 chr6 171115067 1135558 0.0066362245003241 0.0941884261504594 chr7 159138663 1536482 0.009654988743998685 0.11412214171249685 chr8 146364022 1647004 0.011252792711585911 0.11954688418213767 chr9 141213431 1198830 0.008489489926776157 0.10522446881190012 chr10 135534747 1362632 0.01005374658647498 0.1177481697539222 chr11 135006516 1177439 0.008721349419905036 0.108930142225318 chr12 133851895 1291793 0.009650913048335999 0.10958546559639848 chr13 115169878 455280 0.003953116977340203 0.0700002226277518 chr14 107349540 856709 0.007980555855199752 0.09930608479365832 chr15 102531392 537534 0.005242628521028954 0.07994483389194451 chr16 90354753 714646 0.007909334885791786 0.10174280903979827 chr17 81195210 1096318 0.013502249701675751 0.13269606636072162 chr18 78077248 710715 0.00910271581293439 0.11191510272744512 chr19 59128983 723858 0.012242016744986126 0.13425525422798165 chr20 63025520 725833 0.011516493636228626 0.12281038678215107 chr21 48129895 381394 0.007924264119005453 0.10602669523016142 chr22 51304566 316347 0.006166059371791587 0.08934240088247805 chrMT 16571 656 0.03958723070424235 0.2227253654548457 chrX 155270560 743894 0.004790953288247302 0.07655298984148408 chrY 59373566 66048 0.001112414234981271 0.042453434868707986