BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525157.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 = 1,969,236 number of mapped reads = 1,150,890 (58.44%) number of supplementary alignments = 3,820 (0.19%) number of secondary alignments = 0 number of mapped bases = 69,328,428 bp number of sequenced bases = 69,306,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,541 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4241 >>>>>>> ACTG content number of A's = 18,972,735 bp (27.38%) number of C's = 12,730,460 bp (18.37%) number of T's = 20,901,578 bp (30.16%) number of G's = 16,699,973 bp (24.1%) number of N's = 1,656 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 335,313 number of insertions = 5,563 mapped reads with insertion percentage = 0.48% number of deletions = 13,655 mapped reads with deletion percentage = 1.18% homopolymer indels = 42.98% >>>>>>> Coverage mean coverageData = 0.0224X std coverageData = 0.2164X There is a 2.07% of reference with a coverageData >= 1X There is a 0.12% 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 7567432 0.030360734788299686 0.3855652225736795 chr2 243199373 6004649 0.02469023224003131 0.2627608626291076 chr3 198022430 5515940 0.027855127320677762 0.17784860381569856 chr4 191154276 3946037 0.020643205491254615 0.15787974604925673 chr5 180915260 3147693 0.01739871473528546 0.1396529446599112 chr6 171115067 3554390 0.020771928868192537 0.16758376916669504 chr7 159138663 4114137 0.025852529626945526 0.28723316783853514 chr8 146364022 3232304 0.022084006409717274 0.18633563061180095 chr9 141213431 2308300 0.01634617885603247 0.1603051193814169 chr10 135534747 3847886 0.02839040235195186 0.24981716628939532 chr11 135006516 3212339 0.02379395524879703 0.1899007319324559 chr12 133851895 3196027 0.023877338456807055 0.1646499998068067 chr13 115169878 2185460 0.018975968699037782 0.14554706623998706 chr14 107349540 2663953 0.024815690873011657 0.17164923362825604 chr15 102531392 1963979 0.01915490428531391 0.1518933295273834 chr16 90354753 1967973 0.021780514413004926 0.16960002774472818 chr17 81195210 1458029 0.01795708145837667 0.14682809916122933 chr18 78077248 1506519 0.019295236942777492 0.3114007148739477 chr19 59128983 1301744 0.022015328760178404 0.2763292368063635 chr20 63025520 1334508 0.021174089479943998 0.1561933732373602 chr21 48129895 882041 0.018326260632814596 0.1485567433979934 chr22 51304566 592437 0.011547451741429798 0.11402690504238612 chrMT 16571 50945 3.074346750346992 2.3940595979471206 chrX 155270560 3582499 0.02307262239538519 0.16881709158581107 chrY 59373566 191207 0.003220406198947188 0.09914073700329544