BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716733.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 = 753,786 number of mapped reads = 693,305 (91.98%) number of supplementary alignments = 3,776 (0.5%) number of secondary alignments = 0 number of mapped bases = 41,100,106 bp number of sequenced bases = 41,087,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,635 duplication rate = 1.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0671 >>>>>>> ACTG content number of A's = 10,489,236 bp (25.53%) number of C's = 7,987,955 bp (19.44%) number of T's = 12,195,901 bp (29.68%) number of G's = 10,414,383 bp (25.35%) number of N's = 406 bp (0%) GC percentage = 44.79% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 207,012 number of insertions = 2,290 mapped reads with insertion percentage = 0.33% number of deletions = 7,684 mapped reads with deletion percentage = 1.1% homopolymer indels = 44.12% >>>>>>> Coverage mean coverageData = 0.0133X std coverageData = 0.151X There is a 1.26% of reference with a coverageData >= 1X There is a 0.05% 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 2956922 0.011863248276520844 0.20728330268923031 chr2 243199373 4181062 0.01719191109921159 0.17432859452550467 chr3 198022430 3092451 0.015616670293360202 0.13094839900760707 chr4 191154276 2326101 0.01216871026207125 0.11766750668414096 chr5 180915260 2277453 0.012588506906493128 0.11634825544183211 chr6 171115067 2294424 0.01340866143599149 0.12476466322170529 chr7 159138663 2017389 0.012676925656966214 0.24717304356683137 chr8 146364022 3532360 0.024134073057926763 0.19433434531445554 chr9 141213431 1475914 0.010451654559685615 0.11603954380036806 chr10 135534747 1980296 0.014610983853461578 0.18448992298453312 chr11 135006516 1387574 0.01027782984933853 0.12015100644467051 chr12 133851895 1909792 0.014267948914731465 0.12863304965618344 chr13 115169878 1077228 0.009353383182363013 0.09966460357567022 chr14 107349540 1341004 0.012491939881624085 0.11638958394589996 chr15 102531392 986453 0.009620985151552415 0.10128552713586957 chr16 90354753 1280058 0.014167024506170694 0.12645693260987442 chr17 81195210 1723400 0.021225390019928514 0.15345530285152267 chr18 78077248 922949 0.011820972480997281 0.16516856143207598 chr19 59128983 817786 0.01383054398212802 0.19100130847169963 chr20 63025520 922755 0.01464097400545049 0.12704008607162712 chr21 48129895 421144 0.0087501541401659 0.09901611765412272 chr22 51304566 632449 0.012327343340161966 0.11517911487638316 chrMT 16571 9930 0.5992396355078149 0.869825204019455 chrX 155270560 1446053 0.009313117695975336 0.10667602775658094 chrY 59373566 87159 0.0014679765065820705 0.050405149157093675