BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038417.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 = 19,753,886 number of mapped reads = 19,158,425 (96.99%) number of supplementary alignments = 200,147 (1.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,641,192 number of mapped paired reads (second in pair) = 9,517,233 number of mapped paired reads (both in pair) = 19,012,656 number of mapped paired reads (singletons) = 145,769 number of mapped bases = 2,822,278,412 bp number of sequenced bases = 2,821,300,940 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,976,777 duplication rate = 7.87% >>>>>>> Insert size mean insert size = 106,993.2796 std insert size = 3,286,462.4622 median insert size = 283 >>>>>>> Mapping quality mean mapping quality = 54.3256 >>>>>>> ACTG content number of A's = 809,624,113 bp (28.7%) number of C's = 603,978,764 bp (21.41%) number of T's = 803,860,627 bp (28.49%) number of G's = 603,568,436 bp (21.39%) number of N's = 269,000 bp (0.01%) GC percentage = 42.8% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 25,240,713 number of insertions = 334,576 mapped reads with insertion percentage = 1.65% number of deletions = 359,072 mapped reads with deletion percentage = 1.79% homopolymer indels = 44.27% >>>>>>> Coverage mean coverageData = 0.9117X std coverageData = 8.9884X There is a 48.71% of reference with a coverageData >= 1X There is a 23.2% of reference with a coverageData >= 2X There is a 9.48% of reference with a coverageData >= 3X There is a 3.93% of reference with a coverageData >= 4X There is a 1.54% of reference with a coverageData >= 5X There is a 0.64% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% 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 0.03% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 243202996 0.9757367705816067 22.387403090511143 chr2 243199373 240034696 0.9869873143135118 7.426260937388162 chr3 198022430 186149920 0.9400446201978231 1.3017323775192364 chr4 191154276 150142001 0.7854493456374473 6.0608698605551234 chr5 180915260 178315413 0.9856294764742344 1.2890983617923488 chr6 171115067 159897141 0.9344422078273212 4.060824379270787 chr7 159138663 147003848 0.9237469086943378 7.321685708274062 chr8 146364022 156436309 1.068816686384855 5.636100884278305 chr9 141213431 120773813 0.8552572665697783 10.054712013310201 chr10 135534747 145193610 1.071264846939951 19.58988782900155 chr11 135006516 130358253 0.9655700840394993 3.9620595402908965 chr12 133851895 122594483 0.9158965063587632 1.4096325304036055 chr13 115169878 90757584 0.7880323012932253 1.1530964109931252 chr14 107349540 89393192 0.8327300890157517 1.2429840560968437 chr15 102531392 80754596 0.7876085014041359 1.1706191522621208 chr16 90354753 90076420 0.9969195533078377 5.124848280623629 chr17 81195210 83257586 1.025400217574411 5.13480120441448 chr18 78077248 90615142 1.1605831957601784 8.184962661166683 chr19 59128983 58792519 0.9943096602896079 9.008853102012097 chr20 63025520 71575628 1.135661046509414 2.3245605663425875 chr21 48129895 35537830 0.7383733124703472 3.257973712602024 chr22 51304566 29846866 0.5817584735050677 1.0345050782938734 chrMT 16571 3019880 182.23885100476735 24.671637868480428 chrX 155270560 111854480 0.7203843407275661 1.9057958113518192 chrY 59373566 6694206 0.11274724512925499 6.263040290048992