BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926963.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 27,444,214 number of mapped reads = 27,036,325 (98.51%) number of supplementary alignments = 286,483 (1.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,534,376 number of mapped paired reads (second in pair) = 13,501,949 number of mapped paired reads (both in pair) = 26,829,808 number of mapped paired reads (singletons) = 206,517 number of mapped bases = 2,570,750,155 bp number of sequenced bases = 2,568,828,901 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,727,304 duplication rate = 5.07% >>>>>>> Insert size mean insert size = 100,273.6708 std insert size = 3,116,764.5286 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 53.514 >>>>>>> ACTG content number of A's = 727,211,909 bp (28.31%) number of C's = 526,554,541 bp (20.5%) number of T's = 735,842,327 bp (28.65%) number of G's = 578,921,464 bp (22.54%) number of N's = 298,660 bp (0.01%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 24,593,828 number of insertions = 411,686 mapped reads with insertion percentage = 1.5% number of deletions = 1,340,399 mapped reads with deletion percentage = 4.83% homopolymer indels = 52.78% >>>>>>> Coverage mean coverageData = 0.8304X std coverageData = 3.1X There is a 32.7% of reference with a coverageData >= 1X There is a 18.54% of reference with a coverageData >= 2X There is a 10.75% of reference with a coverageData >= 3X There is a 6.65% of reference with a coverageData >= 4X There is a 4.23% of reference with a coverageData >= 5X There is a 2.77% of reference with a coverageData >= 6X There is a 1.85% of reference with a coverageData >= 7X There is a 1.26% of reference with a coverageData >= 8X There is a 0.87% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 210318909 0.8438049548530513 3.864895605872269 chr2 243199373 219073945 0.9007997935915731 5.5065554642362295 chr3 198022430 173556876 0.8764505919859684 1.7653580371866886 chr4 191154276 151802467 0.7941358685588598 2.534159924793785 chr5 180915260 155076270 0.8571762824208417 1.7344693408710448 chr6 171115067 147438545 0.861633914446587 2.3069879286896073 chr7 159138663 131971497 0.8292861992940082 2.3313309171993932 chr8 146364022 131471318 0.8982488743032765 2.1286363175916008 chr9 141213431 111142829 0.7870556519514068 3.7944870731983573 chr10 135534747 126430909 0.9328302283989212 4.531394389325132 chr11 135006516 123505516 0.9148115191714155 3.071446440307468 chr12 133851895 114025539 0.8518784063535297 1.7842433940303797 chr13 115169878 77848008 0.675940700397373 1.5482041915752804 chr14 107349540 77134363 0.7185346392727906 1.6560079611943455 chr15 102531392 77838277 0.7591653198271219 1.7357906332677808 chr16 90354753 84584557 0.9361384342448482 4.594655597360042 chr17 81195210 68852177 0.8479832369421793 3.322612177826311 chr18 78077248 68427522 0.8764079645839976 4.340562337013436 chr19 59128983 43299139 0.7322828298940978 2.5633231873487863 chr20 63025520 61430428 0.9746913313844932 2.069218338836974 chr21 48129895 33462303 0.6952498649747729 2.453584098950933 chr22 51304566 33891325 0.6605908136909295 1.71013822606713 chrMT 16571 46446 2.802848349526281 3.0387971191620777 chrX 155270560 143555210 0.9245488004937962 2.130568776102296 chrY 59373566 4565780 0.07689920460563207 2.247639984612691