BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695949.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 338,325,590 number of mapped reads = 336,520,034 (99.47%) number of supplementary alignments = 2,923,418 (0.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 168,553,952 number of mapped paired reads (second in pair) = 167,966,082 number of mapped paired reads (both in pair) = 335,430,696 number of mapped paired reads (singletons) = 1,089,338 number of mapped bases = 33,416,678,586 bp number of sequenced bases = 33,408,957,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,658,003 duplication rate = 10% >>>>>>> Insert size mean insert size = 58,428.4765 std insert size = 2,334,406.6006 median insert size = 321 >>>>>>> Mapping quality mean mapping quality = 54.126 >>>>>>> ACTG content number of A's = 9,623,005,973 bp (28.8%) number of C's = 7,000,633,293 bp (20.95%) number of T's = 9,576,965,304 bp (28.67%) number of G's = 7,200,569,540 bp (21.55%) number of N's = 7,783,296 bp (0.02%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 137,656,952 number of insertions = 3,335,040 mapped reads with insertion percentage = 0.97% number of deletions = 3,307,882 mapped reads with deletion percentage = 0.96% homopolymer indels = 45.17% >>>>>>> Coverage mean coverageData = 10.7946X std coverageData = 15.4698X There is a 91.32% of reference with a coverageData >= 1X There is a 89.32% of reference with a coverageData >= 2X There is a 86.11% of reference with a coverageData >= 3X There is a 81.76% of reference with a coverageData >= 4X There is a 76.47% of reference with a coverageData >= 5X There is a 70.58% of reference with a coverageData >= 6X There is a 64.39% of reference with a coverageData >= 7X There is a 58.18% of reference with a coverageData >= 8X There is a 52.16% of reference with a coverageData >= 9X There is a 46.46% of reference with a coverageData >= 10X There is a 41.18% of reference with a coverageData >= 11X There is a 36.37% of reference with a coverageData >= 12X There is a 32.03% of reference with a coverageData >= 13X There is a 28.15% of reference with a coverageData >= 14X There is a 24.71% of reference with a coverageData >= 15X There is a 21.68% of reference with a coverageData >= 16X There is a 19.01% of reference with a coverageData >= 17X There is a 16.67% of reference with a coverageData >= 18X There is a 14.63% of reference with a coverageData >= 19X There is a 12.85% of reference with a coverageData >= 20X There is a 11.29% of reference with a coverageData >= 21X There is a 9.94% of reference with a coverageData >= 22X There is a 8.76% of reference with a coverageData >= 23X There is a 7.73% of reference with a coverageData >= 24X There is a 6.83% of reference with a coverageData >= 25X There is a 6.04% of reference with a coverageData >= 26X There is a 5.36% of reference with a coverageData >= 27X There is a 4.76% of reference with a coverageData >= 28X There is a 4.24% of reference with a coverageData >= 29X There is a 3.78% of reference with a coverageData >= 30X There is a 3.37% of reference with a coverageData >= 31X There is a 3.02% of reference with a coverageData >= 32X There is a 2.71% of reference with a coverageData >= 33X There is a 2.43% of reference with a coverageData >= 34X There is a 2.19% of reference with a coverageData >= 35X There is a 1.97% of reference with a coverageData >= 36X There is a 1.78% of reference with a coverageData >= 37X There is a 1.61% of reference with a coverageData >= 38X There is a 1.46% of reference with a coverageData >= 39X There is a 1.33% of reference with a coverageData >= 40X There is a 1.21% of reference with a coverageData >= 41X There is a 1.1% of reference with a coverageData >= 42X There is a 1.01% of reference with a coverageData >= 43X There is a 0.92% of reference with a coverageData >= 44X There is a 0.85% of reference with a coverageData >= 45X There is a 0.78% of reference with a coverageData >= 46X There is a 0.72% of reference with a coverageData >= 47X There is a 0.66% of reference with a coverageData >= 48X There is a 0.61% of reference with a coverageData >= 49X There is a 0.56% of reference with a coverageData >= 50X There is a 0.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2886939169 11.582475331124652 22.102714458584998 chr2 243199373 2956649966 12.157309163786373 22.460096102554463 chr3 198022430 2235631915 11.289791338284253 8.52530410664893 chr4 191154276 1970952543 10.31079494659068 14.079322942369279 chr5 180915260 1986888906 10.982428491659576 8.435918862730402 chr6 171115067 1968061354 11.501391364911191 11.58160542210373 chr7 159138663 1741249033 10.941709576886417 10.379404659881809 chr8 146364022 1690141098 11.547517449336013 10.096497967275846 chr9 141213431 1393768506 9.869942937651588 13.75363361113132 chr10 135534747 1574960223 11.6203428114268 17.595954998005382 chr11 135006516 1643368984 12.1725160584101 11.02340698964947 chr12 133851895 1623318305 12.127720007251298 10.05126775506716 chr13 115169878 1001309206 8.694193511258213 8.59066108658309 chr14 107349540 1057642975 9.852328896798253 9.738735424747112 chr15 102531392 1061727808 10.355148674856574 10.019602973718158 chr16 90354753 1041450547 11.526239765162105 14.664465971451055 chr17 81195210 1036226932 12.762168260910958 17.49227453693956 chr18 78077248 876089538 11.220804529380954 24.380701037737094 chr19 59128983 743436443 12.57313089589246 17.732083332409793 chr20 63025520 799761719 12.689490209680143 11.513076173630953 chr21 48129895 415912553 8.6414598037249 21.0718833221016 chr22 51304566 448474666 8.741418180986074 10.79507709758259 chrMT 16571 32302299 1949.327077424416 597.084599787352 chrX 155270560 1033468572 6.655920942128373 6.48070243590559 chrY 59373566 196945326 3.317054023671073 18.147570571549224