BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432731.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 381,909,958 number of mapped reads = 381,753,076 (99.96%) number of supplementary alignments = 2,325,106 (0.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 190,880,713 number of mapped paired reads (second in pair) = 190,872,363 number of mapped paired reads (both in pair) = 381,697,302 number of mapped paired reads (singletons) = 55,774 number of mapped bases = 53,490,708,848 bp number of sequenced bases = 53,435,382,812 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 192,190,795 duplication rate = 33.62% >>>>>>> Insert size mean insert size = 46,017.3214 std insert size = 2,111,233.1372 median insert size = 317 >>>>>>> Mapping quality mean mapping quality = 57.425 >>>>>>> ACTG content number of A's = 15,061,451,426 bp (28.19%) number of C's = 11,185,676,315 bp (20.93%) number of T's = 14,900,556,458 bp (27.89%) number of G's = 12,279,892,312 bp (22.98%) number of N's = 7,806,301 bp (0.01%) GC percentage = 43.91% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 473,940,114 number of insertions = 11,629,815 mapped reads with insertion percentage = 2.98% number of deletions = 39,416,170 mapped reads with deletion percentage = 9.81% homopolymer indels = 53.43% >>>>>>> Coverage mean coverageData = 17.2791X std coverageData = 54.2288X There is a 42.76% of reference with a coverageData >= 1X There is a 38.31% of reference with a coverageData >= 2X There is a 35.39% of reference with a coverageData >= 3X There is a 33.15% of reference with a coverageData >= 4X There is a 31.28% of reference with a coverageData >= 5X There is a 29.66% of reference with a coverageData >= 6X There is a 28.24% of reference with a coverageData >= 7X There is a 26.97% of reference with a coverageData >= 8X There is a 25.82% of reference with a coverageData >= 9X There is a 24.78% of reference with a coverageData >= 10X There is a 23.84% of reference with a coverageData >= 11X There is a 22.97% of reference with a coverageData >= 12X There is a 22.17% of reference with a coverageData >= 13X There is a 21.42% of reference with a coverageData >= 14X There is a 20.72% of reference with a coverageData >= 15X There is a 20.08% of reference with a coverageData >= 16X There is a 19.47% of reference with a coverageData >= 17X There is a 18.9% of reference with a coverageData >= 18X There is a 18.36% of reference with a coverageData >= 19X There is a 17.85% of reference with a coverageData >= 20X There is a 17.37% of reference with a coverageData >= 21X There is a 16.91% of reference with a coverageData >= 22X There is a 16.47% of reference with a coverageData >= 23X There is a 16.06% of reference with a coverageData >= 24X There is a 15.66% of reference with a coverageData >= 25X There is a 15.28% of reference with a coverageData >= 26X There is a 14.92% of reference with a coverageData >= 27X There is a 14.57% of reference with a coverageData >= 28X There is a 14.24% of reference with a coverageData >= 29X There is a 13.92% of reference with a coverageData >= 30X There is a 13.61% of reference with a coverageData >= 31X There is a 13.32% of reference with a coverageData >= 32X There is a 13.03% of reference with a coverageData >= 33X There is a 12.76% of reference with a coverageData >= 34X There is a 12.49% of reference with a coverageData >= 35X There is a 12.24% of reference with a coverageData >= 36X There is a 11.99% of reference with a coverageData >= 37X There is a 11.76% of reference with a coverageData >= 38X There is a 11.53% of reference with a coverageData >= 39X There is a 11.3% of reference with a coverageData >= 40X There is a 11.09% of reference with a coverageData >= 41X There is a 10.88% of reference with a coverageData >= 42X There is a 10.67% of reference with a coverageData >= 43X There is a 10.48% of reference with a coverageData >= 44X There is a 10.29% of reference with a coverageData >= 45X There is a 10.1% of reference with a coverageData >= 46X There is a 9.92% of reference with a coverageData >= 47X There is a 9.75% of reference with a coverageData >= 48X There is a 9.57% of reference with a coverageData >= 49X There is a 9.41% of reference with a coverageData >= 50X There is a 9.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3089567469 12.395425361848948 41.078317095604795 chr2 243199373 4995052338 20.538919473283347 60.54682310900316 chr3 198022430 1991936119 10.059143901021718 34.513894221666675 chr4 191154276 2420978079 12.665047989823675 40.30803291218403 chr5 180915260 2541929806 14.05038914904138 43.52894564068122 chr6 171115067 3488041845 20.38418887449578 57.44280471239492 chr7 159138663 2000622028 12.571564887408913 39.37031975255691 chr8 146364022 4459429941 30.46807459964444 78.25373558629931 chr9 141213431 2082085822 14.744247818750328 46.65120133649322 chr10 135534747 3448175102 25.441262689633383 68.54037725984834 chr11 135006516 3653133625 27.058943029090536 70.70138363114242 chr12 133851895 3030290159 22.639127813618177 61.73186185198432 chr13 115169878 1324198934 11.49778880550694 38.37026802013507 chr14 107349540 1906552178 17.76022680674738 54.162368809232284 chr15 102531392 3074782504 29.988693648087796 84.21307628950966 chr16 90354753 2358088434 26.098111673217677 75.36469724596866 chr17 81195210 1353700937 16.67217729962149 50.17416702428836 chr18 78077248 1937897127 24.82025400024345 67.67695792412762 chr19 59128983 678080739 11.46782346992168 39.311100754881004 chr20 63025520 1429219706 22.67684115894641 61.005301760698245 chr21 48129895 405797605 8.431300442271898 31.618243121199267 chr22 51304566 762293689 14.858203634350986 50.00180495283764 chrMT 16571 4870475 293.9155754028121 448.9841540467207 chrX 155270560 912522051 5.876980484903255 23.799273629856625 chrY 59373566 141462136 2.3825777282772607 22.109643254362695