BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716572.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 = 1,436,102 number of mapped reads = 1,350,567 (94.04%) number of supplementary alignments = 35,252 (2.45%) number of secondary alignments = 0 number of mapped bases = 104,378,112 bp number of sequenced bases = 104,338,449 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,143 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.035 >>>>>>> ACTG content number of A's = 26,827,868 bp (25.71%) number of C's = 21,726,374 bp (20.82%) number of T's = 29,819,539 bp (28.58%) number of G's = 25,960,481 bp (24.88%) number of N's = 4,187 bp (0%) GC percentage = 45.7% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 658,112 number of insertions = 9,494 mapped reads with insertion percentage = 0.69% number of deletions = 19,199 mapped reads with deletion percentage = 1.4% homopolymer indels = 38.54% >>>>>>> Coverage mean coverageData = 0.0337X std coverageData = 0.2765X There is a 2.91% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.06% 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% 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 11808947 0.04737780372470968 0.49321685164523466 chr2 243199373 9473381 0.03895314730108289 0.2957392536779627 chr3 198022430 6540828 0.03303074303249384 0.20381406862851098 chr4 191154276 5001697 0.026165760477155114 0.23199272882245872 chr5 180915260 5352437 0.029585326301385523 0.19427888673899651 chr6 171115067 6413018 0.03747781018021049 0.22765234210831334 chr7 159138663 6513537 0.040929946734565695 0.34587418847758755 chr8 146364022 6242953 0.04265360376609492 0.299854302578839 chr9 141213431 3211069 0.02273911891567878 0.20210602135229558 chr10 135534747 5350383 0.039476098332186356 0.35785057290472705 chr11 135006516 3346429 0.02478716656905656 0.22382950847112762 chr12 133851895 3929863 0.029359786053085014 0.19236985466259568 chr13 115169878 1945231 0.016890102115068664 0.14344679570249141 chr14 107349540 2038035 0.01898503710402485 0.15848550227813488 chr15 102531392 2248924 0.021934004368145125 0.16590844032902155 chr16 90354753 3355474 0.037136662860447416 0.22727300392283242 chr17 81195210 2926868 0.03604729884927941 0.23006590220152176 chr18 78077248 2971830 0.03806268888985431 0.30767231492694236 chr19 59128983 2843134 0.0480835937935885 0.38564475919410063 chr20 63025520 2886763 0.04580308103764951 0.2520829046017528 chr21 48129895 1562559 0.03246545624086651 0.23783879562771015 chr22 51304566 1796044 0.03500748841730773 0.21772923998631744 chrMT 16571 61698 3.7232514633999156 3.411421751487525 chrX 155270560 6227832 0.04010954813327137 0.23307389212433507 chrY 59373566 329178 0.00554418442712368 0.18906854707394274