BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038421.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 = 16,728,918 number of mapped reads = 16,089,564 (96.18%) number of supplementary alignments = 250,154 (1.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,150,556 number of mapped paired reads (second in pair) = 7,939,008 number of mapped paired reads (both in pair) = 15,822,028 number of mapped paired reads (singletons) = 267,536 number of mapped bases = 2,182,226,220 bp number of sequenced bases = 2,180,669,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,188,393 duplication rate = 13.42% >>>>>>> Insert size mean insert size = 72,281.2857 std insert size = 2,553,489.9411 median insert size = 249 >>>>>>> Mapping quality mean mapping quality = 53.4692 >>>>>>> ACTG content number of A's = 626,991,611 bp (28.75%) number of C's = 431,848,818 bp (19.8%) number of T's = 639,452,075 bp (29.32%) number of G's = 482,199,691 bp (22.11%) number of N's = 177,694 bp (0.01%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0138 number of mismatches = 29,169,547 number of insertions = 386,790 mapped reads with insertion percentage = 2.29% number of deletions = 782,859 mapped reads with deletion percentage = 4.68% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.7049X std coverageData = 10.8922X There is a 27.99% of reference with a coverageData >= 1X There is a 15.71% of reference with a coverageData >= 2X There is a 8.56% of reference with a coverageData >= 3X There is a 5.11% of reference with a coverageData >= 4X There is a 3% of reference with a coverageData >= 5X There is a 1.84% of reference with a coverageData >= 6X There is a 1.14% of reference with a coverageData >= 7X There is a 0.72% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% 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 168518608 0.676101055732174 17.548622161971213 chr2 243199373 193665498 0.7963240020359756 9.670808955272864 chr3 198022430 149088050 0.7528846605912269 1.679271573704565 chr4 191154276 149522040 0.7822060961900742 8.401139672044932 chr5 180915260 129772020 0.7173083132954069 1.546917762989054 chr6 171115067 124296251 0.7263898684035813 6.747808276962812 chr7 159138663 113375770 0.7124338477067638 11.245801954408167 chr8 146364022 111106896 0.7591134384104312 3.544621396639486 chr9 141213431 91350454 0.6468963564804258 16.42302444888902 chr10 135534747 120529250 0.8892867155313317 28.145869534104396 chr11 135006516 100452418 0.7440560720787729 8.07980721571106 chr12 133851895 90525333 0.6763096854176028 1.6094145512922406 chr13 115169878 65690288 0.5703773342540139 1.3630008052028741 chr14 107349540 63488801 0.5914212673850302 1.5547935850029257 chr15 102531392 57742769 0.5631716089448976 1.359789966129988 chr16 90354753 77699472 0.8599378496447221 17.113247992981755 chr17 81195210 52696207 0.6490063514830493 13.053839518802844 chr18 78077248 61064386 0.7821021816752558 12.22896458050386 chr19 59128983 26808464 0.4533895670081117 8.039501893223601 chr20 63025520 43599224 0.6917709524649698 2.699781065094684 chr21 48129895 27865430 0.5789630332665384 3.9667172617488142 chr22 51304566 18927998 0.3689339853298827 1.1515102908407322 chrMT 16571 6304292 380.4412527910205 199.8761300785943 chrX 155270560 130296827 0.8391598961193931 4.044802906686071 chrY 59373566 7839474 0.13203643520417824 9.650079782109193