BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094026.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 420,060 number of mapped reads = 389,959 (92.83%) number of supplementary alignments = 19,516 (4.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 195,898 number of mapped paired reads (second in pair) = 194,061 number of mapped paired reads (both in pair) = 385,976 number of mapped paired reads (singletons) = 3,983 number of mapped bases = 50,370,903 bp number of sequenced bases = 49,387,444 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 362,227 duplication rate = 47.35% >>>>>>> Insert size mean insert size = 729,509.7111 std insert size = 7,788,081.4706 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 45.412 >>>>>>> ACTG content number of A's = 13,575,138 bp (27.49%) number of C's = 11,010,692 bp (22.29%) number of T's = 13,182,015 bp (26.69%) number of G's = 11,619,003 bp (23.53%) number of N's = 596 bp (0%) GC percentage = 45.82% >>>>>>> Mismatches and indels general error rate = 0.0362 number of mismatches = 1,722,263 number of insertions = 30,541 mapped reads with insertion percentage = 7.71% number of deletions = 124,846 mapped reads with deletion percentage = 30.88% homopolymer indels = 28.54% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 4.8998X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% 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 658701 0.0026427256123064983 0.9076311335832714 chr2 243199373 3809396 0.01566367525133381 5.081503287299694 chr3 198022430 726879 0.0036706902344345537 0.8394991428850416 chr4 191154276 682676 0.00357133522872384 0.9397297511333016 chr5 180915260 548833 0.0030336468023758746 1.5791288962164118 chr6 171115067 1257520 0.0073489729574777885 2.9591001039625002 chr7 159138663 1660158 0.010432147466263432 2.9755244783183605 chr8 146364022 1078642 0.007369584309455503 2.301126816271189 chr9 141213431 588370 0.00416653002362077 1.3143456170754106 chr10 135534747 673758 0.004971108995392893 0.958826560761745 chr11 135006516 1275703 0.00944919577066932 2.7448426937700066 chr12 133851895 1393377 0.010409841414647137 2.4411521417734585 chr13 115169878 593500 0.005153257173720372 1.7423034294247894 chr14 107349540 255424 0.00237936743837002 0.40250031096716427 chr15 102531392 664287 0.006478864541310431 1.5688602623098253 chr16 90354753 261772 0.0028971580498925163 0.6352011412573556 chr17 81195210 987005 0.012155951071497938 2.9573684904513637 chr18 78077248 194116 0.002486204431795547 0.7759197690294753 chr19 59128983 297560 0.0050323882621150446 1.081452443965607 chr20 63025520 1054260 0.016727509745258745 6.582500933364228 chr21 48129895 157834 0.003279333977354407 0.4787513371176562 chr22 51304566 251679 0.004905586765903058 1.0892838606812756 chrMT 16571 5926630 357.65071510470096 1489.0027040122382 chrX 155270560 24342424 0.15677423975285462 10.003505650246632 chrY 59373566 1030399 0.017354507559812056 6.526019135144198