BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716592.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 = 931,732 number of mapped reads = 701,650 (75.31%) number of supplementary alignments = 3,650 (0.39%) number of secondary alignments = 0 number of mapped bases = 40,551,687 bp number of sequenced bases = 40,540,189 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,412 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7668 >>>>>>> ACTG content number of A's = 10,440,547 bp (25.75%) number of C's = 7,761,484 bp (19.15%) number of T's = 12,833,102 bp (31.66%) number of G's = 9,504,473 bp (23.44%) number of N's = 583 bp (0%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 201,750 number of insertions = 3,150 mapped reads with insertion percentage = 0.45% number of deletions = 7,319 mapped reads with deletion percentage = 1.03% homopolymer indels = 40.99% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 0.1451X There is a 1.22% of reference with a coverageData >= 1X There is a 0.06% 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 3235289 0.012980063949369257 0.2201010602818371 chr2 243199373 3449949 0.014185682131672272 0.17967211815878928 chr3 198022430 2676058 0.01351391355009632 0.12217549880086791 chr4 191154276 2580284 0.013498437251803878 0.12760989833368327 chr5 180915260 2453038 0.013559044162443787 0.12274920477544213 chr6 171115067 2356308 0.01377031281529405 0.13312950024174341 chr7 159138663 2213359 0.013908367446822147 0.16394445102994307 chr8 146364022 2062382 0.0140907715695323 0.1394680225281937 chr9 141213431 1700917 0.012045008664933578 0.12893809270849224 chr10 135534747 1947549 0.014369370534922678 0.14488421449010255 chr11 135006516 1838491 0.013617794566300785 0.13766014874572927 chr12 133851895 1835670 0.013714187610119378 0.1242259229001958 chr13 115169878 1247878 0.01083510742279331 0.10924042020416973 chr14 107349540 1228433 0.011443300083074414 0.11671725087595501 chr15 102531392 1176374 0.011473305658427031 0.11355041747532564 chr16 90354753 1199229 0.013272450647947652 0.12510222339056642 chr17 81195210 1121297 0.013809891002190893 0.127183181756639 chr18 78077248 1048459 0.013428483032598689 0.1825820705430664 chr19 59128983 869724 0.01470892878370663 0.1713940077513985 chr20 63025520 873808 0.013864352091025984 0.12542606114670884 chr21 48129895 536509 0.011147105141201742 0.11595444068136425 chr22 51304566 492702 0.009603472720147365 0.10314339069465467 chrMT 16571 1367 0.08249351276326111 0.33486945460807666 chrX 155270560 2282288 0.014698781275729282 0.1344805995486279 chrY 59373566 124325 0.0020939453089275453 0.0635216073012391