BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173966.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,754,794 number of mapped reads = 4,647,297 (97.74%) number of supplementary alignments = 638,584 (13.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,322,547 number of mapped paired reads (second in pair) = 2,324,750 number of mapped paired reads (both in pair) = 4,577,324 number of mapped paired reads (singletons) = 69,973 number of mapped bases = 528,680,413 bp number of sequenced bases = 528,323,989 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,620,302 duplication rate = 63.5% >>>>>>> Insert size mean insert size = 1,128,247.94 std insert size = 9,538,872.2934 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 52.4286 >>>>>>> ACTG content number of A's = 157,244,432 bp (29.76%) number of C's = 105,418,358 bp (19.95%) number of T's = 155,882,937 bp (29.51%) number of G's = 109,773,925 bp (20.78%) number of N's = 4,337 bp (0%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 4,570,144 number of insertions = 59,375 mapped reads with insertion percentage = 1.23% number of deletions = 148,816 mapped reads with deletion percentage = 3.12% homopolymer indels = 40.81% >>>>>>> Coverage mean coverageData = 0.1708X std coverageData = 3.0551X There is a 4.01% of reference with a coverageData >= 1X There is a 2.96% of reference with a coverageData >= 2X There is a 2.15% of reference with a coverageData >= 3X There is a 1.68% of reference with a coverageData >= 4X There is a 1.22% of reference with a coverageData >= 5X There is a 0.99% of reference with a coverageData >= 6X There is a 0.72% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.44% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 42088117 0.1688586244284623 1.6823045491200583 chr2 243199373 47376616 0.1948056667070437 9.770847507107165 chr3 198022430 33906519 0.17122564852880556 1.1759839128926681 chr4 191154276 34961437 0.1828964422433323 1.5570724423493911 chr5 180915260 32764998 0.18110687843579365 1.2087176964594242 chr6 171115067 30929713 0.1807538841684818 1.3229283783134635 chr7 159138663 26716352 0.16788096303159214 1.3606425072034982 chr8 146364022 28021264 0.1914491253868386 1.7693001445330072 chr9 141213431 22323061 0.15808029620072045 1.4837801094697534 chr10 135534747 26181600 0.19317260392274166 1.8187954551342547 chr11 135006516 25563119 0.18934729787412632 1.272663728493719 chr12 133851895 24142090 0.18036420029764988 1.2535858871691703 chr13 115169878 18444871 0.16015360370530218 1.1522178282374653 chr14 107349540 16093005 0.14991219338247747 1.1109294758543016 chr15 102531392 15156933 0.14782724299695454 1.1065171800530291 chr16 90354753 17021712 0.18838756606417817 1.5343157907474778 chr17 81195210 15236620 0.1876541731956848 1.2927266333862453 chr18 78077248 14815716 0.18975714922739081 1.97753075286552 chr19 59128983 11003766 0.18609767057891052 1.4814157275614537 chr20 63025520 11875795 0.1884283541016401 1.268142307089886 chr21 48129895 7778687 0.1616186156234083 1.4238553715155327 chr22 51304566 7010821 0.13665101464848178 1.2874990992950623 chrMT 16571 713993 43.086898799106876 36.709606235225294 chrX 155270560 14391686 0.09268779606385139 0.8727870052078179 chrY 59373566 4161922 0.07009722137962877 1.1351278662026771