BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708610.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 2,374,715 number of mapped reads = 1,480,690 (62.35%) number of supplementary alignments = 406 (0.02%) number of secondary alignments = 0 number of mapped bases = 71,348,254 bp number of sequenced bases = 71,329,454 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,590 duplication rate = 3.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.6185 >>>>>>> ACTG content number of A's = 20,579,771 bp (28.85%) number of C's = 13,652,953 bp (19.14%) number of T's = 22,296,237 bp (31.26%) number of G's = 14,794,569 bp (20.74%) number of N's = 5,924 bp (0.01%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 489,452 number of insertions = 3,518 mapped reads with insertion percentage = 0.24% number of deletions = 12,214 mapped reads with deletion percentage = 0.82% homopolymer indels = 49.39% >>>>>>> Coverage mean coverageData = 0.023X std coverageData = 0.2288X There is a 1.74% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% 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 5811891 0.02331745845479759 0.26845970895455346 chr2 243199373 5964282 0.024524249081842822 0.2563083437504417 chr3 198022430 4933264 0.024912652571731395 0.20501687795379273 chr4 191154276 5039879 0.026365504897206692 0.21854637490289652 chr5 180915260 4298448 0.02375945511727424 0.19950555514247842 chr6 171115067 4118004 0.024065700771984035 0.23319028496398203 chr7 159138663 4066862 0.02555546165421787 0.28636702396228014 chr8 146364022 3477970 0.02376246534138014 0.24889524113603362 chr9 141213431 3083696 0.02183712964243465 0.21576312119233626 chr10 135534747 3602742 0.026581685359253298 0.2350075841405574 chr11 135006516 3217108 0.023829279469740557 0.2400571276311563 chr12 133851895 3205913 0.023951196208316664 0.202727694895564 chr13 115169878 2471715 0.021461471028040857 0.19094186064171845 chr14 107349540 2197106 0.020466841311103896 0.19340661196461234 chr15 102531392 2087360 0.020358252816854373 0.18510062952225925 chr16 90354753 1818754 0.020129035159888047 0.18875251611798338 chr17 81195210 1703916 0.02098542512544767 0.21036397824246947 chr18 78077248 1886627 0.024163595007856833 0.3325325367188892 chr19 59128983 1252920 0.021189608486924257 0.2790450450066561 chr20 63025520 1273975 0.020213637269474335 0.19128636993407394 chr21 48129895 952898 0.019798464135440147 0.19137078712022978 chr22 51304566 772131 0.015049947016411755 0.1578130773514182 chrMT 16571 574 0.03463882686621206 0.1925091214349709 chrX 155270560 3909802 0.02518057511997123 0.21469099691332896 chrY 59373566 200417 0.003375525734802589 0.08706333971261647