BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716409.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 = 1,197,750 number of mapped reads = 996,897 (83.23%) number of supplementary alignments = 4,718 (0.39%) number of secondary alignments = 0 number of mapped bases = 57,339,728 bp number of sequenced bases = 57,323,551 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,624 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0889 >>>>>>> ACTG content number of A's = 14,452,467 bp (25.21%) number of C's = 11,367,271 bp (19.83%) number of T's = 17,807,299 bp (31.06%) number of G's = 13,695,701 bp (23.89%) number of N's = 813 bp (0%) GC percentage = 43.72% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 285,571 number of insertions = 3,711 mapped reads with insertion percentage = 0.37% number of deletions = 10,367 mapped reads with deletion percentage = 1.03% homopolymer indels = 43.49% >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 0.2027X There is a 1.71% of reference with a coverageData >= 1X There is a 0.1% 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 5973758 0.023966873085543888 0.3957640629361437 chr2 243199373 5449939 0.022409346425412043 0.26264174458666395 chr3 198022430 3888286 0.01963558370635084 0.1491818840865435 chr4 191154276 2612753 0.013668294817532619 0.12922223690763798 chr5 180915260 2485329 0.013737531040775665 0.12579442518726178 chr6 171115067 3888818 0.022726333035301912 0.1724452613125095 chr7 159138663 4222890 0.02653591478269489 0.272492577701414 chr8 146364022 3255182 0.022240315314647475 0.17381466988663316 chr9 141213431 2393604 0.01695025737318145 0.164073423208169 chr10 135534747 3061195 0.02258605315432507 0.19300948133444623 chr11 135006516 1933120 0.01431871629070111 0.15866446649858304 chr12 133851895 2298012 0.017168318760074335 0.1418963352063023 chr13 115169878 1309203 0.011367581721324738 0.11458851669480441 chr14 107349540 1266312 0.0117961567417988 0.12392344362781499 chr15 102531392 1718152 0.016757326380587908 0.1389950672343959 chr16 90354753 1225003 0.013557704042420436 0.1316312403824123 chr17 81195210 1384711 0.017054097156716512 0.141453036822786 chr18 78077248 1955331 0.02504354405524129 0.260692734710284 chr19 59128983 1489312 0.02518751252664028 0.25854788987070276 chr20 63025520 879260 0.013950856732320495 0.1263335997851351 chr21 48129895 737516 0.01532344917851992 0.13595580544143052 chr22 51304566 746135 0.014543247476257766 0.1281530110685735 chrMT 16571 8163 0.4926075674370889 0.7292195833416928 chrX 155270560 3027004 0.019495028548876234 0.1617479219544002 chrY 59373566 130740 0.0022019900236411602 0.060667951513278626