BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975293.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 55,580,498 number of mapped reads = 55,296,177 (99.49%) number of supplementary alignments = 101,153 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,738,268 number of mapped paired reads (second in pair) = 27,557,909 number of mapped paired reads (both in pair) = 55,065,216 number of mapped paired reads (singletons) = 230,961 number of mapped bases = 5,274,899,743 bp number of sequenced bases = 5,272,833,594 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,798,650 duplication rate = 59.39% >>>>>>> Insert size mean insert size = 109,940.5105 std insert size = 3,289,205.755 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 56.4134 >>>>>>> ACTG content number of A's = 1,438,629,134 bp (27.28%) number of C's = 1,145,493,427 bp (21.72%) number of T's = 1,503,444,682 bp (28.51%) number of G's = 1,184,112,483 bp (22.46%) number of N's = 1,153,868 bp (0.02%) GC percentage = 44.18% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 47,080,741 number of insertions = 546,399 mapped reads with insertion percentage = 0.98% number of deletions = 1,474,258 mapped reads with deletion percentage = 2.62% homopolymer indels = 49.52% >>>>>>> Coverage mean coverageData = 1.7039X std coverageData = 25.8421X There is a 8.14% of reference with a coverageData >= 1X There is a 5.22% of reference with a coverageData >= 2X There is a 3.26% of reference with a coverageData >= 3X There is a 2.63% of reference with a coverageData >= 4X There is a 2.25% of reference with a coverageData >= 5X There is a 2.04% of reference with a coverageData >= 6X There is a 1.9% of reference with a coverageData >= 7X There is a 1.79% of reference with a coverageData >= 8X There is a 1.7% of reference with a coverageData >= 9X There is a 1.63% of reference with a coverageData >= 10X There is a 1.56% of reference with a coverageData >= 11X There is a 1.51% of reference with a coverageData >= 12X There is a 1.46% of reference with a coverageData >= 13X There is a 1.41% of reference with a coverageData >= 14X There is a 1.37% of reference with a coverageData >= 15X There is a 1.33% of reference with a coverageData >= 16X There is a 1.29% of reference with a coverageData >= 17X There is a 1.26% of reference with a coverageData >= 18X There is a 1.23% of reference with a coverageData >= 19X There is a 1.2% of reference with a coverageData >= 20X There is a 1.17% of reference with a coverageData >= 21X There is a 1.14% of reference with a coverageData >= 22X There is a 1.12% of reference with a coverageData >= 23X There is a 1.09% of reference with a coverageData >= 24X There is a 1.07% of reference with a coverageData >= 25X There is a 1.05% of reference with a coverageData >= 26X There is a 1.03% of reference with a coverageData >= 27X There is a 1.01% of reference with a coverageData >= 28X There is a 0.99% of reference with a coverageData >= 29X There is a 0.97% of reference with a coverageData >= 30X There is a 0.95% of reference with a coverageData >= 31X There is a 0.94% of reference with a coverageData >= 32X There is a 0.92% of reference with a coverageData >= 33X There is a 0.9% of reference with a coverageData >= 34X There is a 0.89% of reference with a coverageData >= 35X There is a 0.87% of reference with a coverageData >= 36X There is a 0.86% of reference with a coverageData >= 37X There is a 0.84% of reference with a coverageData >= 38X There is a 0.83% of reference with a coverageData >= 39X There is a 0.82% of reference with a coverageData >= 40X There is a 0.8% of reference with a coverageData >= 41X There is a 0.79% of reference with a coverageData >= 42X There is a 0.78% of reference with a coverageData >= 43X There is a 0.77% of reference with a coverageData >= 44X There is a 0.76% of reference with a coverageData >= 45X There is a 0.75% of reference with a coverageData >= 46X There is a 0.74% of reference with a coverageData >= 47X There is a 0.73% of reference with a coverageData >= 48X There is a 0.72% of reference with a coverageData >= 49X There is a 0.71% of reference with a coverageData >= 50X There is a 0.7% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 623988150 2.503456751668434 31.54663005014277 chr2 243199373 420620523 1.7295296357528027 23.57347493497386 chr3 198022430 371246621 1.8747705550325788 28.106909186687243 chr4 191154276 240646948 1.2589148045006329 20.859847332061165 chr5 180915260 250361816 1.3838623452770098 20.532901869075154 chr6 171115067 434554584 2.539546000353084 41.04607359263421 chr7 159138663 290530587 1.8256442621991866 29.10862165573629 chr8 146364022 189075060 1.2918137764757516 19.891389665898284 chr9 141213431 207426549 1.4688868298936806 22.21852988577036 chr10 135534747 236089307 1.7419098218407416 24.771436072966523 chr11 135006516 235670180 1.7456207817406384 23.8429563650498 chr12 133851895 295395946 2.206886544265959 29.149760198873462 chr13 115169878 113653356 0.9868323034951899 18.535400303976374 chr14 107349540 175110457 1.631217581370167 22.764784248047874 chr15 102531392 196413708 1.9156446057028076 24.661669110276858 chr16 90354753 162781370 1.801580598643217 26.67514085320489 chr17 81195210 174927448 2.154406004984777 30.58937593023196 chr18 78077248 101802241 1.3038656408586533 21.29011369619657 chr19 59128983 170444273 2.8825842142422777 36.99221954667858 chr20 63025520 132261348 2.0985364023969972 29.48253452076335 chr21 48129895 44942416 0.9337734063205415 15.741016336184737 chr22 51304566 78026805 1.52085498588956 23.991103130073554 chrMT 16571 37150 2.241868324180798 4.42056856780767 chrX 155270560 123070293 0.7926183366634345 14.26345454252481 chrY 59373566 5822607 0.09806732848082596 4.06238256598735