BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926994.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 = 29,517,494 number of mapped reads = 28,799,700 (97.57%) number of supplementary alignments = 673,827 (2.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,432,108 number of mapped paired reads (second in pair) = 14,367,592 number of mapped paired reads (both in pair) = 28,379,364 number of mapped paired reads (singletons) = 420,336 number of mapped bases = 2,620,903,364 bp number of sequenced bases = 2,618,859,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,107,764 duplication rate = 8.16% >>>>>>> Insert size mean insert size = 240,291.1897 std insert size = 4,770,806.2999 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.0579 >>>>>>> ACTG content number of A's = 753,788,448 bp (28.78%) number of C's = 498,414,068 bp (19.03%) number of T's = 772,324,096 bp (29.49%) number of G's = 593,848,578 bp (22.68%) number of N's = 484,233 bp (0.02%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 25,252,051 number of insertions = 452,479 mapped reads with insertion percentage = 1.54% number of deletions = 1,426,930 mapped reads with deletion percentage = 4.82% homopolymer indels = 52.47% >>>>>>> Coverage mean coverageData = 0.8466X std coverageData = 3.5727X There is a 32.24% of reference with a coverageData >= 1X There is a 18.35% of reference with a coverageData >= 2X There is a 10.95% of reference with a coverageData >= 3X There is a 6.91% of reference with a coverageData >= 4X There is a 4.49% of reference with a coverageData >= 5X There is a 3% of reference with a coverageData >= 6X There is a 2.04% of reference with a coverageData >= 7X There is a 1.41% of reference with a coverageData >= 8X There is a 0.99% of reference with a coverageData >= 9X There is a 0.71% of reference with a coverageData >= 10X There is a 0.51% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% 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 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 227190077 0.9114925214168272 4.345732817001629 chr2 243199373 225023300 0.9252626650480715 5.238565500233883 chr3 198022430 156648969 0.7910667948070327 1.7806722108384134 chr4 191154276 161343633 0.8440493007857172 2.510348336036057 chr5 180915260 160001353 0.8843994309822178 1.83742328932124 chr6 171115067 143954446 0.8412727676400349 2.605856759102187 chr7 159138663 140186957 0.8809107375748155 2.7793773572666134 chr8 146364022 144010086 0.9839172498279666 2.3759138014951677 chr9 141213431 116302649 0.8235948108930233 4.048253611150099 chr10 135534747 122465018 0.90356916370678 7.0291107051392725 chr11 135006516 120466262 0.8922996131534866 2.4121371008954453 chr12 133851895 122188334 0.9128621899600301 1.9442960781998142 chr13 115169878 87685895 0.7613613604765649 1.7243439431673528 chr14 107349540 85153843 0.7932390115504919 1.842770677411957 chr15 102531392 74128577 0.7229842056567417 1.7377041136436333 chr16 90354753 72990896 0.8078257488015047 3.97235095842333 chr17 81195210 63878926 0.786732690265842 2.366331188121894 chr18 78077248 74668366 0.9563396240605202 3.8123995180084083 chr19 59128983 39911596 0.6749920931330748 2.8807866627686622 chr20 63025520 61310538 0.9727890860718007 2.1021553564325526 chr21 48129895 34836431 0.7238002700816197 2.935097787602312 chr22 51304566 27959247 0.5449660562375677 1.5649777915270093 chrMT 16571 7442344 449.1185806529479 372.2427163154044 chrX 155270560 146621319 0.9442956797476612 2.175920724986811 chrY 59373566 4534302 0.07636903601174974 2.6473921540327767