BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16352028.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 1,594,243,576 number of mapped reads = 1,549,291,278 (97.18%) number of supplementary alignments = 35,069,329 (2.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 776,192,274 number of mapped paired reads (second in pair) = 773,099,004 number of mapped paired reads (both in pair) = 1,534,909,976 number of mapped paired reads (singletons) = 14,381,302 number of mapped bases = 140,056,973,705 bp number of sequenced bases = 139,967,773,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 590,326,322 duplication rate = 34.43% >>>>>>> Insert size mean insert size = 162,209.496 std insert size = 3,936,033.4252 median insert size = 287 >>>>>>> Mapping quality mean mapping quality = 52.8987 >>>>>>> ACTG content number of A's = 40,770,017,711 bp (29.13%) number of C's = 28,974,371,496 bp (20.7%) number of T's = 40,360,414,656 bp (28.84%) number of G's = 29,860,074,407 bp (21.33%) number of N's = 2,894,883 bp (0%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,067,808,447 number of insertions = 18,043,753 mapped reads with insertion percentage = 1.14% number of deletions = 59,042,305 mapped reads with deletion percentage = 3.73% homopolymer indels = 45.11% >>>>>>> Coverage mean coverageData = 45.2425X std coverageData = 429.0109X There is a 91.81% of reference with a coverageData >= 1X There is a 91.74% of reference with a coverageData >= 2X There is a 91.7% of reference with a coverageData >= 3X There is a 91.67% of reference with a coverageData >= 4X There is a 91.65% of reference with a coverageData >= 5X There is a 91.62% of reference with a coverageData >= 6X There is a 91.6% of reference with a coverageData >= 7X There is a 91.58% of reference with a coverageData >= 8X There is a 91.55% of reference with a coverageData >= 9X There is a 91.53% of reference with a coverageData >= 10X There is a 91.5% of reference with a coverageData >= 11X There is a 91.47% of reference with a coverageData >= 12X There is a 91.44% of reference with a coverageData >= 13X There is a 91.4% of reference with a coverageData >= 14X There is a 91.36% of reference with a coverageData >= 15X There is a 91.31% of reference with a coverageData >= 16X There is a 91.25% of reference with a coverageData >= 17X There is a 91.19% of reference with a coverageData >= 18X There is a 91.1% of reference with a coverageData >= 19X There is a 91% of reference with a coverageData >= 20X There is a 90.88% of reference with a coverageData >= 21X There is a 90.72% of reference with a coverageData >= 22X There is a 90.53% of reference with a coverageData >= 23X There is a 90.28% of reference with a coverageData >= 24X There is a 89.97% of reference with a coverageData >= 25X There is a 89.57% of reference with a coverageData >= 26X There is a 89.08% of reference with a coverageData >= 27X There is a 88.47% of reference with a coverageData >= 28X There is a 87.73% of reference with a coverageData >= 29X There is a 86.83% of reference with a coverageData >= 30X There is a 85.76% of reference with a coverageData >= 31X There is a 84.49% of reference with a coverageData >= 32X There is a 83.02% of reference with a coverageData >= 33X There is a 81.34% of reference with a coverageData >= 34X There is a 79.43% of reference with a coverageData >= 35X There is a 77.3% of reference with a coverageData >= 36X There is a 74.96% of reference with a coverageData >= 37X There is a 72.4% of reference with a coverageData >= 38X There is a 69.65% of reference with a coverageData >= 39X There is a 66.73% of reference with a coverageData >= 40X There is a 63.66% of reference with a coverageData >= 41X There is a 60.47% of reference with a coverageData >= 42X There is a 57.19% of reference with a coverageData >= 43X There is a 53.84% of reference with a coverageData >= 44X There is a 50.47% of reference with a coverageData >= 45X There is a 47.1% of reference with a coverageData >= 46X There is a 43.76% of reference with a coverageData >= 47X There is a 40.49% of reference with a coverageData >= 48X There is a 37.3% of reference with a coverageData >= 49X There is a 34.22% of reference with a coverageData >= 50X There is a 31.27% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11472688660 46.0287264840957 961.7458321107562 chr2 243199373 11962576749 49.18835357770433 472.247999296547 chr3 198022430 9164769802 46.281473275527425 38.13547439206791 chr4 191154276 8956682070 46.85577669212066 284.2338981402507 chr5 180915260 8411511581 46.494207182965106 30.49178567070362 chr6 171115067 7551045907 44.12846886826161 108.21624090507419 chr7 159138663 7538147787 47.36842477431144 286.38145974808793 chr8 146364022 6953634828 47.50918110189675 613.8153684342772 chr9 141213431 5930829848 41.99904928306713 296.97567784371074 chr10 135534747 7267768912 53.62292012099303 908.0507860484684 chr11 135006516 6320149646 46.813663764199354 156.51581899219784 chr12 133851895 6229329769 46.538973310762614 43.628229853306024 chr13 115169878 4385249000 38.076353610446645 25.143871327999854 chr14 107349540 4186535076 38.99909655877426 42.241803994386 chr15 102531392 3940112115 38.42834899773915 27.774419441749103 chr16 90354753 4569241458 50.57001769458658 369.79610966643776 chr17 81195210 3992154098 49.167359724791645 166.7679395896236 chr18 78077248 3767860751 48.25811420761141 486.9700728133142 chr19 59128983 2933468435 49.611346012834346 393.9568795844603 chr20 63025520 2951053874 46.82315788905827 52.8950140260369 chr21 48129895 1897044015 39.41508733812945 98.33079300411688 chr22 51304566 1746601916 34.04379087818421 37.448210296705994 chrMT 16571 569665998 34377.285498762896 11647.223581065628 chrX 155270560 6903212461 44.459248817032666 80.74776947154307 chrY 59373566 455638949 7.674104482792898 285.40811932168776