BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524654.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 = 1,002,368 number of mapped reads = 921,152 (91.9%) number of supplementary alignments = 3,478 (0.35%) number of secondary alignments = 0 number of mapped bases = 53,422,202 bp number of sequenced bases = 53,405,525 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,838 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6761 >>>>>>> ACTG content number of A's = 13,985,927 bp (26.19%) number of C's = 10,869,422 bp (20.35%) number of T's = 16,347,162 bp (30.61%) number of G's = 12,202,494 bp (22.85%) number of N's = 520 bp (0%) GC percentage = 43.2% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 275,674 number of insertions = 4,033 mapped reads with insertion percentage = 0.44% number of deletions = 9,997 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.87% >>>>>>> Coverage mean coverageData = 0.0173X std coverageData = 0.1842X There is a 1.57% of reference with a coverageData >= 1X There is a 0.11% 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 5862933 0.023522240291630005 0.31372381012346484 chr2 243199373 4519439 0.0185832674823549 0.21905844431310556 chr3 198022430 3358858 0.016962007788713634 0.14114426636251257 chr4 191154276 2406241 0.012587952780088478 0.1409658439769034 chr5 180915260 3244074 0.01793145586502764 0.14400011099455604 chr6 171115067 3449607 0.02015957484328367 0.15796977847016416 chr7 159138663 3231402 0.02030557464215971 0.22140984404425826 chr8 146364022 4704144 0.032140029603723246 0.2427044151085384 chr9 141213431 1946335 0.013782931171752352 0.15118658201328547 chr10 135534747 2318692 0.017107731052908522 0.20566567724286658 chr11 135006516 2661434 0.01971337442705358 0.17361394745368708 chr12 133851895 1783550 0.013324802013449268 0.12713066306149848 chr13 115169878 1285942 0.011165610507983693 0.11405596677284888 chr14 107349540 977263 0.009103560201562113 0.10539452426089 chr15 102531392 1405079 0.013703890804486493 0.1259468259743428 chr16 90354753 1588354 0.01757908629333534 0.149066902206002 chr17 81195210 1196029 0.01473029012425733 0.1327332339326122 chr18 78077248 1382772 0.017710306592773353 0.22921219937323814 chr19 59128983 1101129 0.018622491782075805 0.21807588355534696 chr20 63025520 1009733 0.016021018152646737 0.1401379779827466 chr21 48129895 466693 0.009696530607432242 0.11783578747272347 chr22 51304566 993339 0.019361610036814268 0.1502509535425936 chrMT 16571 4134 0.2494719691026492 0.5811536785367012 chrX 155270560 2367330 0.015246483299860579 0.141008127236865 chrY 59373566 157696 0.0026559967780948176 0.09713869964941621