BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716246.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 = 2,124,866 number of mapped reads = 1,896,164 (89.24%) number of supplementary alignments = 27,125 (1.28%) number of secondary alignments = 0 number of mapped bases = 147,215,997 bp number of sequenced bases = 147,151,643 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,685 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.852 >>>>>>> ACTG content number of A's = 36,890,999 bp (25.07%) number of C's = 27,401,944 bp (18.62%) number of T's = 47,065,368 bp (31.98%) number of G's = 35,785,580 bp (24.32%) number of N's = 7,752 bp (0.01%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,316,163 number of insertions = 13,835 mapped reads with insertion percentage = 0.72% number of deletions = 37,490 mapped reads with deletion percentage = 1.95% homopolymer indels = 43.7% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.5043X There is a 3.99% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11631347 0.04666526788713598 0.7408949350946398 chr2 243199373 12598598 0.05180357927978704 0.8204761247788932 chr3 198022430 9769313 0.04933437590883013 0.25741023712324723 chr4 191154276 9423673 0.049298782099962024 0.289853574406795 chr5 180915260 8937611 0.0494021952598139 0.2661134123199207 chr6 171115067 8405052 0.04911929818547189 0.32716853045952216 chr7 159138663 8250540 0.05184497497003604 0.6581339633853546 chr8 146364022 7492907 0.05119363965005006 0.678892687197679 chr9 141213431 6305219 0.044650278343566344 0.5505268630152534 chr10 135534747 6970904 0.05143259683806397 0.4548447570405502 chr11 135006516 6564522 0.04862374198294251 0.5176172398552048 chr12 133851895 6660715 0.04976182817583569 0.2645522684684317 chr13 115169878 4632445 0.04022271344248537 0.2312579185664591 chr14 107349540 4445620 0.04141256683540517 0.31052090307120445 chr15 102531392 4177819 0.04074673052327232 0.24218451594323112 chr16 90354753 4342714 0.04806292813395218 0.2985219973033727 chr17 81195210 4043675 0.04980189102288177 0.294618245757318 chr18 78077248 4032006 0.05164124124866696 1.0191654509339256 chr19 59128983 3113859 0.05266214370708862 0.5686413443747056 chr20 63025520 3016972 0.04786905367857338 0.28895941615667897 chr21 48129895 1929358 0.04008647847663079 0.2577542073388759 chr22 51304566 1636274 0.03189334064340394 0.20555518688148017 chrMT 16571 15390 0.92873091545471 1.2455731404744854 chrX 155270560 8429302 0.05428783151165295 0.38614284471479277 chrY 59373566 390162 0.006571308181152535 0.1778973442156365