BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365343.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 510,014,896 number of mapped reads = 488,468,428 (95.78%) number of supplementary alignments = 2,359,533 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 244,823,078 number of mapped paired reads (second in pair) = 243,645,350 number of mapped paired reads (both in pair) = 485,304,404 number of mapped paired reads (singletons) = 3,164,024 number of mapped bases = 49,729,563,836 bp number of sequenced bases = 49,712,297,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 347,755,175 duplication rate = 41.64% >>>>>>> Insert size mean insert size = 62,611.0704 std insert size = 2,427,186.2972 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.4457 >>>>>>> ACTG content number of A's = 14,818,148,222 bp (29.81%) number of C's = 9,798,112,213 bp (19.71%) number of T's = 14,339,437,317 bp (28.84%) number of G's = 10,734,184,411 bp (21.59%) number of N's = 22,414,945 bp (0.05%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 314,501,734 number of insertions = 15,261,129 mapped reads with insertion percentage = 3.05% number of deletions = 8,116,418 mapped reads with deletion percentage = 1.62% homopolymer indels = 49.4% >>>>>>> Coverage mean coverageData = 16.0641X std coverageData = 185.2744X There is a 81.55% of reference with a coverageData >= 1X There is a 76.49% of reference with a coverageData >= 2X There is a 71.87% of reference with a coverageData >= 3X There is a 68.25% of reference with a coverageData >= 4X There is a 64.64% of reference with a coverageData >= 5X There is a 61.55% of reference with a coverageData >= 6X There is a 58.4% of reference with a coverageData >= 7X There is a 55.62% of reference with a coverageData >= 8X There is a 52.77% of reference with a coverageData >= 9X There is a 50.2% of reference with a coverageData >= 10X There is a 47.59% of reference with a coverageData >= 11X There is a 45.21% of reference with a coverageData >= 12X There is a 42.82% of reference with a coverageData >= 13X There is a 40.62% of reference with a coverageData >= 14X There is a 38.41% of reference with a coverageData >= 15X There is a 36.39% of reference with a coverageData >= 16X There is a 34.38% of reference with a coverageData >= 17X There is a 32.54% of reference with a coverageData >= 18X There is a 30.72% of reference with a coverageData >= 19X There is a 29.04% of reference with a coverageData >= 20X There is a 27.4% of reference with a coverageData >= 21X There is a 25.89% of reference with a coverageData >= 22X There is a 24.42% of reference with a coverageData >= 23X There is a 23.07% of reference with a coverageData >= 24X There is a 21.75% of reference with a coverageData >= 25X There is a 20.54% of reference with a coverageData >= 26X There is a 19.37% of reference with a coverageData >= 27X There is a 18.3% of reference with a coverageData >= 28X There is a 17.26% of reference with a coverageData >= 29X There is a 16.3% of reference with a coverageData >= 30X There is a 15.38% of reference with a coverageData >= 31X There is a 14.53% of reference with a coverageData >= 32X There is a 13.71% of reference with a coverageData >= 33X There is a 12.95% of reference with a coverageData >= 34X There is a 12.22% of reference with a coverageData >= 35X There is a 11.55% of reference with a coverageData >= 36X There is a 10.91% of reference with a coverageData >= 37X There is a 10.31% of reference with a coverageData >= 38X There is a 9.74% of reference with a coverageData >= 39X There is a 9.21% of reference with a coverageData >= 40X There is a 8.71% of reference with a coverageData >= 41X There is a 8.24% of reference with a coverageData >= 42X There is a 7.79% of reference with a coverageData >= 43X There is a 7.37% of reference with a coverageData >= 44X There is a 6.97% of reference with a coverageData >= 45X There is a 6.6% of reference with a coverageData >= 46X There is a 6.25% of reference with a coverageData >= 47X There is a 5.92% of reference with a coverageData >= 48X There is a 5.61% of reference with a coverageData >= 49X There is a 5.32% of reference with a coverageData >= 50X There is a 5.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4343273141 17.42532525525784 512.3538641501636 chr2 243199373 4266776514 17.544356555557403 107.39438797040307 chr3 198022430 3360176145 16.96866433262131 31.074484089054845 chr4 191154276 3273098093 17.12280866267412 94.56359801590793 chr5 180915260 2728754522 15.083053369848404 20.642288432970528 chr6 171115067 3111659218 18.184600997175778 74.72621369482462 chr7 159138663 2587389931 16.25871351577209 130.12889039069 chr8 146364022 2224954648 15.20151344296893 67.23834259740869 chr9 141213431 2032975045 14.396470864021426 138.44565651118592 chr10 135534747 2440575607 18.00701046057215 326.0476770090634 chr11 135006516 2214013794 16.399310637717665 109.44209291428511 chr12 133851895 2137921511 15.972291695982339 37.526868127278306 chr13 115169878 1733125410 15.048426203941972 19.324062179780928 chr14 107349540 1482329718 13.808440334257604 21.499955492125626 chr15 102531392 1463331242 14.272031359917555 24.694321105062006 chr16 90354753 1289108669 14.26719266223881 50.48295421939918 chr17 81195210 1738970377 21.41715474348795 99.86040383916215 chr18 78077248 1451123340 18.585738831368648 180.37084470402564 chr19 59128983 1068105421 18.063991071857266 250.01482630441936 chr20 63025520 1172948083 18.610684735326263 31.934396945713974 chr21 48129895 821965412 17.078063685781988 68.49951292139781 chr22 51304566 687995367 13.410022160600676 64.23465132369708 chrMT 16571 184629189 11141.704725122201 2132.699120311019 chrX 155270560 1375793640 8.860621356682168 42.535075038733495 chrY 59373566 538569799 9.070868322108192 203.5604838052487