BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716828.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 = 755,524 number of mapped reads = 571,064 (75.59%) number of supplementary alignments = 695 (0.09%) number of secondary alignments = 0 number of mapped bases = 29,850,592 bp number of sequenced bases = 29,843,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,214 duplication rate = 5.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6453 >>>>>>> ACTG content number of A's = 6,297,495 bp (21.1%) number of C's = 5,431,902 bp (18.2%) number of T's = 9,773,698 bp (32.75%) number of G's = 8,339,434 bp (27.94%) number of N's = 484 bp (0%) GC percentage = 46.15% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 199,111 number of insertions = 1,710 mapped reads with insertion percentage = 0.3% number of deletions = 4,439 mapped reads with deletion percentage = 0.77% homopolymer indels = 40.84% >>>>>>> Coverage mean coverageData = 0.0096X std coverageData = 0.1198X There is a 0.86% of reference with a coverageData >= 1X There is a 0.08% 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 2937119 0.011783798123415708 0.13652159128888014 chr2 243199373 2601711 0.010697852415927075 0.17414171738312767 chr3 198022430 2017372 0.010187593395354253 0.11251089884044384 chr4 191154276 1896299 0.00992025415115485 0.11241954332084116 chr5 180915260 1830824 0.010119787573475007 0.11091076022810452 chr6 171115067 1274945 0.007450805018823971 0.10866407072920253 chr7 159138663 1702278 0.010696822305211903 0.1247657757431991 chr8 146364022 1848035 0.012626292819419788 0.12783733283051557 chr9 141213431 1305839 0.009247271953897926 0.10956072599721527 chr10 135534747 1527606 0.011270954746386917 0.12835379749150275 chr11 135006516 1267365 0.009387435788654823 0.11359274655183936 chr12 133851895 1433176 0.01070717751138301 0.11502996060860522 chr13 115169878 506017 0.004393657515205495 0.07434754689738968 chr14 107349540 948727 0.008837736985179442 0.1046259797377642 chr15 102531392 574416 0.005602342743966648 0.0822133105814341 chr16 90354753 796254 0.008812530315920403 0.1067726689897935 chr17 81195210 1191612 0.014675890363483265 0.1380800462650619 chr18 78077248 789857 0.010116352973916293 0.12057998916289156 chr19 59128983 806484 0.013639402524477717 0.14598173739153522 chr20 63025520 792852 0.012579856540652103 0.12794297247112704 chr21 48129895 415605 0.008635069741997152 0.10894307431239492 chr22 51304566 342741 0.006680516506074722 0.09446872272184118 chrMT 16571 13823 0.8341681250377165 1.1641291032084546 chrX 155270560 940235 0.00605546215586522 0.08729440810205685 chrY 59373566 89400 0.0015057205760556811 0.052529839435243066