BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046413.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 5,853,148 number of mapped reads = 5,813,818 (99.33%) number of supplementary alignments = 47,957 (0.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,905,949 number of mapped paired reads (second in pair) = 2,907,869 number of mapped paired reads (both in pair) = 5,786,296 number of mapped paired reads (singletons) = 27,522 number of mapped bases = 550,131,977 bp number of sequenced bases = 549,999,107 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,525,972 duplication rate = 40.98% >>>>>>> Insert size mean insert size = 15,058.2836 std insert size = 1,211,555.784 median insert size = 122 >>>>>>> Mapping quality mean mapping quality = 52.124 >>>>>>> ACTG content number of A's = 164,658,471 bp (29.94%) number of C's = 110,939,330 bp (20.17%) number of T's = 163,873,419 bp (29.8%) number of G's = 110,482,025 bp (20.09%) number of N's = 45,862 bp (0.01%) GC percentage = 40.26% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 1,846,836 number of insertions = 43,650 mapped reads with insertion percentage = 0.74% number of deletions = 49,984 mapped reads with deletion percentage = 0.84% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.1777X std coverageData = 22.7204X There is a 1.56% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% 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 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% 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 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 89323244 0.3583671873780407 25.009880888719426 chr2 243199373 55471209 0.2280894408391423 19.33203070873162 chr3 198022430 40021977 0.2021083015696757 26.460780846458665 chr4 191154276 7933937 0.04150541209970108 2.0055574768444018 chr5 180915260 38543157 0.2130453616792746 19.9114831008074 chr6 171115067 37682586 0.22021781401634258 17.114659156241558 chr7 159138663 48583853 0.30529257996845177 28.49084011223731 chr8 146364022 60605317 0.41407250341890717 65.91752971551456 chr9 141213431 14281775 0.10113609519196513 16.988407031519316 chr10 135534747 19628888 0.14482550367692795 14.93232733072063 chr11 135006516 21238174 0.15731221447118893 13.678019015599267 chr12 133851895 11483577 0.08579315967099307 8.917248536207126 chr13 115169878 6229329 0.05408817920255156 4.245067735518912 chr14 107349540 34245029 0.31900489745927185 23.504442850004843 chr15 102531392 3435925 0.03351095633228114 1.4748979286777808 chr16 90354753 6414896 0.0709967742372114 8.779531970627035 chr17 81195210 33053836 0.40709096016870944 39.54405005198154 chr18 78077248 2041475 0.02614686163118864 0.41785180908582703 chr19 59128983 988771 0.016722273068691205 0.8915381777732754 chr20 63025520 2322749 0.036854102909424626 1.5264977602039782 chr21 48129895 477000 0.00991068025392534 0.5894251872206959 chr22 51304566 2019018 0.039353573325228014 4.030823062004888 chrMT 16571 27809 1.678172711363225 1.8183565541955715 chrX 155270560 13979979 0.09003625027178365 11.71763790312966 chrY 59373566 98467 0.0016584316326898742 0.11557165922229447