BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173961.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 10,909,564 number of mapped reads = 10,640,328 (97.53%) number of supplementary alignments = 1,361,027 (12.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,331,055 number of mapped paired reads (second in pair) = 5,309,273 number of mapped paired reads (both in pair) = 10,460,672 number of mapped paired reads (singletons) = 179,656 number of mapped bases = 1,207,031,663 bp number of sequenced bases = 1,206,187,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,696,338 duplication rate = 66.65% >>>>>>> Insert size mean insert size = 988,722.7833 std insert size = 9,394,795.9352 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 52.6094 >>>>>>> ACTG content number of A's = 358,848,455 bp (29.75%) number of C's = 240,710,487 bp (19.96%) number of T's = 356,016,578 bp (29.52%) number of G's = 250,603,057 bp (20.78%) number of N's = 8,789 bp (0%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 10,440,865 number of insertions = 133,644 mapped reads with insertion percentage = 1.21% number of deletions = 353,732 mapped reads with deletion percentage = 3.24% homopolymer indels = 41.26% >>>>>>> Coverage mean coverageData = 0.3899X std coverageData = 6.5741X There is a 7.68% of reference with a coverageData >= 1X There is a 5.99% of reference with a coverageData >= 2X There is a 4.65% of reference with a coverageData >= 3X There is a 3.8% of reference with a coverageData >= 4X There is a 2.92% of reference with a coverageData >= 5X There is a 2.41% of reference with a coverageData >= 6X There is a 1.84% of reference with a coverageData >= 7X There is a 1.57% of reference with a coverageData >= 8X There is a 1.2% of reference with a coverageData >= 9X There is a 1.06% of reference with a coverageData >= 10X There is a 0.81% of reference with a coverageData >= 11X There is a 0.73% of reference with a coverageData >= 12X There is a 0.56% of reference with a coverageData >= 13X There is a 0.51% of reference with a coverageData >= 14X There is a 0.39% of reference with a coverageData >= 15X There is a 0.36% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.18% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% 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 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% 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% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 98228994 0.39409728892912166 3.038095836250745 chr2 243199373 109331779 0.44955617134753056 21.68781903245834 chr3 198022430 85744767 0.43300532671980646 2.0388359092091592 chr4 191154276 82077033 0.42937586706143055 3.0532631302637636 chr5 180915260 73776174 0.4077940910014998 1.9647972916523284 chr6 171115067 70480973 0.41189226779194144 2.3813614967796823 chr7 159138663 65780230 0.41335165672467666 3.0150807906919215 chr8 146364022 60865254 0.41584846582037766 3.5507811214827028 chr9 141213431 52212996 0.36974525461391844 2.9423962455185233 chr10 135534747 59071468 0.4358400285352656 3.7587576444595014 chr11 135006516 56096595 0.4155102780372467 2.122927278086233 chr12 133851895 55075284 0.4114643576768188 2.127208713917634 chr13 115169878 39302053 0.3412528838486744 1.8118980049981823 chr14 107349540 37403950 0.34843139523466987 1.89005465656349 chr15 102531392 35084284 0.34218090007009755 1.90147943458266 chr16 90354753 37201936 0.41173192073249315 2.597488636593364 chr17 81195210 33498788 0.41257098786985097 2.1524478463399688 chr18 78077248 33632969 0.4307652979777156 3.6911591439845854 chr19 59128983 22854273 0.38651557731003083 2.48243303998278 chr20 63025520 25467983 0.40409000988805804 2.1791727565263934 chr21 48129895 17179822 0.3569470076757907 2.734584012891644 chr22 51304566 14955731 0.29150877136354686 2.035686776543698 chrMT 16571 1184941 71.50690966145676 51.291480851155406 chrX 155270560 31461018 0.2026206255712609 1.411401138924525 chrY 59373566 9062368 0.1526330421184404 2.3104968809047604