BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013223.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 = 1,901,965 number of mapped reads = 1,711,114 (89.97%) number of supplementary alignments = 12,068 (0.63%) number of secondary alignments = 0 number of mapped bases = 113,974,454 bp number of sequenced bases = 113,921,262 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,103 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4245 >>>>>>> ACTG content number of A's = 31,720,816 bp (27.84%) number of C's = 21,019,615 bp (18.45%) number of T's = 36,110,918 bp (31.7%) number of G's = 25,068,256 bp (22%) number of N's = 1,657 bp (0%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 835,892 number of insertions = 8,319 mapped reads with insertion percentage = 0.48% number of deletions = 31,354 mapped reads with deletion percentage = 1.81% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.3565X There is a 3.14% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 5540798 0.022229826259891245 0.567142907104108 chr2 243199373 14025996 0.057672829608816464 0.4141562380026647 chr3 198022430 6109971 0.030854944058609925 0.19813438315826132 chr4 191154276 4465414 0.023360262158090568 0.180561934910508 chr5 180915260 3212601 0.017757490440552113 0.1547871990308828 chr6 171115067 5075749 0.02966278241295958 0.27444752076390977 chr7 159138663 9199392 0.05780739781633078 0.6953447820697659 chr8 146364022 5504850 0.03761067730155707 0.39239829217003913 chr9 141213431 5086304 0.03601855690341523 0.3195658780776841 chr10 135534747 4237690 0.031266447120014175 0.33920164940874176 chr11 135006516 6470317 0.04792596084769716 0.3139155431143813 chr12 133851895 5837853 0.04361427232688787 0.24019817990499204 chr13 115169878 1341985 0.011652222120092894 0.12167745381800654 chr14 107349540 4234071 0.03944191097605076 0.23194323688483995 chr15 102531392 1802316 0.01757818717607969 0.14850280174759828 chr16 90354753 4626952 0.051208728333306384 0.2808816633868023 chr17 81195210 5618468 0.06919703760849932 0.4379858705577142 chr18 78077248 1501695 0.01923345197822546 0.4720393187565861 chr19 59128983 2403912 0.040655392297208964 0.4626935602849416 chr20 63025520 4571887 0.07254025036207555 0.3084364442312817 chr21 48129895 2934133 0.06096279661528453 0.28962157958325674 chr22 51304566 1238369 0.024137598201298495 0.1720231257860975 chrMT 16571 4242 0.2559893790356647 0.5756978199126641 chrX 155270560 8675130 0.05587105501519413 0.3032915205538882 chrY 59373566 254359 0.004284044519070995 0.09458747545209546