BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068136.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,650,762 number of mapped reads = 1,158,025 (70.15%) number of supplementary alignments = 9,739 (0.59%) number of secondary alignments = 0 number of mapped bases = 76,841,746 bp number of sequenced bases = 76,812,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 267,373 duplication rate = 13.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5977 >>>>>>> ACTG content number of A's = 21,373,712 bp (27.83%) number of C's = 13,755,713 bp (17.91%) number of T's = 24,880,413 bp (32.39%) number of G's = 16,719,714 bp (21.77%) number of N's = 82,616 bp (0.11%) GC percentage = 39.68% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 689,967 number of insertions = 6,171 mapped reads with insertion percentage = 0.53% number of deletions = 17,380 mapped reads with deletion percentage = 1.48% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 0.5098X There is a 0.71% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 6261889 0.025122862181354406 0.7718719893720314 chr2 243199373 6243401 0.025671945297326075 0.49419316986372036 chr3 198022430 4809548 0.024287895063200667 0.43545458598252657 chr4 191154276 5538395 0.02897342981749464 0.4915075374923576 chr5 180915260 4433831 0.024507777840299377 0.4333920242653858 chr6 171115067 4448239 0.02599560096014222 0.47682970135483277 chr7 159138663 4722579 0.029675874554758577 0.5508187489540033 chr8 146364022 4380118 0.029926193200676052 0.5675144995541892 chr9 141213431 3066590 0.021715993856136814 0.4649688360790188 chr10 135534747 3554325 0.026224455932322654 0.5150016613800562 chr11 135006516 3578201 0.02650391333704219 0.4700559346773751 chr12 133851895 3718424 0.02778013714337029 0.4751095999180163 chr13 115169878 2842583 0.024681653305215795 0.4388088980748778 chr14 107349540 2198648 0.020481205601812547 0.4094124144140127 chr15 102531392 1944594 0.018965840237495264 0.42695071835570997 chr16 90354753 1981074 0.02192550955233091 0.4263202411282587 chr17 81195210 1714024 0.021109915227757892 0.39108063650387026 chr18 78077248 2124173 0.027206043430219262 0.7662992265141196 chr19 59128983 1334017 0.02256113554329186 0.6078609477696235 chr20 63025520 1439506 0.022840049554529656 0.424705872047331 chr21 48129895 974815 0.020253835999434446 0.3831081583168912 chr22 51304566 947627 0.018470617215629502 0.35998016764410035 chrMT 16571 20950 1.2642568342284715 2.6161719671010752 chrX 155270560 4350608 0.02801952926556071 0.48231899236019254 chrY 59373566 213587 0.0035973416183222007 0.14281471735748355