BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038431.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 17,532,914 number of mapped reads = 16,217,822 (92.5%) number of supplementary alignments = 269,169 (1.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,230,071 number of mapped paired reads (second in pair) = 7,987,751 number of mapped paired reads (both in pair) = 15,914,970 number of mapped paired reads (singletons) = 302,852 number of mapped bases = 2,192,834,712 bp number of sequenced bases = 2,191,265,304 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,155,625 duplication rate = 13.08% >>>>>>> Insert size mean insert size = 99,258.1378 std insert size = 3,037,547.3623 median insert size = 262 >>>>>>> Mapping quality mean mapping quality = 53.4995 >>>>>>> ACTG content number of A's = 630,847,333 bp (28.79%) number of C's = 431,905,324 bp (19.71%) number of T's = 643,208,523 bp (29.35%) number of G's = 485,130,169 bp (22.14%) number of N's = 173,955 bp (0.01%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 29,479,766 number of insertions = 398,054 mapped reads with insertion percentage = 2.33% number of deletions = 784,282 mapped reads with deletion percentage = 4.65% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.7083X std coverageData = 10.6201X There is a 28.94% of reference with a coverageData >= 1X There is a 15.87% of reference with a coverageData >= 2X There is a 8.6% of reference with a coverageData >= 3X There is a 5.01% of reference with a coverageData >= 4X There is a 2.9% of reference with a coverageData >= 5X There is a 1.74% of reference with a coverageData >= 6X There is a 1.06% of reference with a coverageData >= 7X There is a 0.66% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171856993 0.689494743525634 16.64154657441696 chr2 243199373 194855363 0.8012165516561591 9.849984872711028 chr3 198022430 145630223 0.735422865985434 1.6355460881897403 chr4 191154276 145723803 0.7623360881553076 8.820392474009848 chr5 180915260 131479812 0.726748047677128 1.5333722862668304 chr6 171115067 125993750 0.7363100877610035 6.909148277612677 chr7 159138663 114295433 0.7182128518950797 10.320275204426169 chr8 146364022 110783199 0.7569018498275485 3.3331557873930207 chr9 141213431 91649382 0.649013208948942 16.224702039983033 chr10 135534747 125338402 0.9247695131640302 28.61255281293172 chr11 135006516 99404876 0.7362968762189227 6.911261993823895 chr12 133851895 93483211 0.6984078260528176 1.6411369524718113 chr13 115169878 66910965 0.5809762601294064 1.3344750680017474 chr14 107349540 62831942 0.5853023869501444 1.5018204243042879 chr15 102531392 58774954 0.5732386233476671 1.340356012497207 chr16 90354753 76566678 0.8474006674557563 15.408242106882094 chr17 81195210 54674925 0.6733762373420796 12.088892053734584 chr18 78077248 61175666 0.7835274368276914 12.036985676409339 chr19 59128983 29753032 0.5031886308614508 7.52100067344696 chr20 63025520 44339654 0.7035190506956547 2.805612531463359 chr21 48129895 28037766 0.5825436768561411 4.339317108221744 chr22 51304566 20387433 0.3973804787667437 1.2030541115814768 chrMT 16571 3128796 188.81153822943696 97.00094737212116 chrX 155270560 127724781 0.8225949658454249 3.6647374828984898 chrY 59373566 8033673 0.13530723419913837 10.102432454578874