BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038475.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 = 15,088,896 number of mapped reads = 14,718,047 (97.54%) number of supplementary alignments = 166,307 (1.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,433,003 number of mapped paired reads (second in pair) = 7,285,044 number of mapped paired reads (both in pair) = 14,552,902 number of mapped paired reads (singletons) = 165,145 number of mapped bases = 2,161,740,337 bp number of sequenced bases = 2,160,923,715 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,557,322 duplication rate = 7.67% >>>>>>> Insert size mean insert size = 102,426.9028 std insert size = 3,204,894.2177 median insert size = 262 >>>>>>> Mapping quality mean mapping quality = 54.3914 >>>>>>> ACTG content number of A's = 630,143,534 bp (29.16%) number of C's = 454,206,328 bp (21.02%) number of T's = 623,703,729 bp (28.86%) number of G's = 452,821,790 bp (20.96%) number of N's = 48,334 bp (0%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 23,338,003 number of insertions = 281,216 mapped reads with insertion percentage = 1.79% number of deletions = 292,750 mapped reads with deletion percentage = 1.9% homopolymer indels = 44.35% >>>>>>> Coverage mean coverageData = 0.6983X std coverageData = 7.2285X There is a 39.51% of reference with a coverageData >= 1X There is a 17.05% of reference with a coverageData >= 2X There is a 6.16% of reference with a coverageData >= 3X There is a 2.53% of reference with a coverageData >= 4X There is a 0.93% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% 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 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% 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 0.01% 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 155288659 0.6230221548776 17.657988570448374 chr2 243199373 214664284 0.8826679170755921 5.7995905374560115 chr3 198022430 139760135 0.7057793149998209 1.0976770497353279 chr4 191154276 117256888 0.6134149361116045 6.192167337972629 chr5 180915260 124404453 0.687639356680028 1.1660664008353747 chr6 171115067 139895142 0.817550110885326 6.301613922974635 chr7 159138663 150557480 0.9460773212603903 5.662696980590757 chr8 146364022 95739727 0.6541206349194203 4.799876124244257 chr9 141213431 89122005 0.6311156408344756 8.19326953136351 chr10 135534747 90604446 0.6684960720810583 12.676373554682414 chr11 135006516 113091376 0.8376734645904054 4.335893683357618 chr12 133851895 78329265 0.5851935454481239 1.023856366550645 chr13 115169878 116732289 1.0135661427026952 1.3504742178743392 chr14 107349540 47145146 0.4391741781101251 0.9483386136821313 chr15 102531392 45925317 0.4479146932873007 0.8693574187757145 chr16 90354753 77086732 0.8531563580280055 5.646895513910622 chr17 81195210 63911121 0.7871292038040175 3.3609176691626232 chr18 78077248 38393977 0.4917434717985962 8.039207265518783 chr19 59128983 46186560 0.7811154134005653 7.9709247136342505 chr20 63025520 68013687 1.0791451938833667 2.4306377944345336 chr21 48129895 22746788 0.47261245843150085 3.2814431015345624 chr22 51304566 20834764 0.4060996052476109 2.1646193428315197 chrMT 16571 3479900 209.9993965361173 26.3667877268145 chrX 155270560 82496461 0.5313078087694152 1.3878194001305515 chrY 59373566 20073735 0.3380921233533455 7.781173838429574