Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A25 F36 I0 R2 1302 104.9 4551290 96.3% 4382892 111.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,028,171 A→G 11.4% intergenic (‑154/+17) yedQ ← / ← yodC putative membrane‑anchored diguanylate cyclase/uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,028,1710AG11.4% 102.7 / 4.7 35intergenic (‑154/+17)yedQ/yodCputative membrane‑anchored diguanylate cyclase/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base A (16/15);  new base G (2/2);  total (18/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.32e-01

AACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATACCGCTGGAGTATCCAGTGACAATC  >  NC_000913/2028080‑2028317
                                                                                           |                                                                                                                                                  
aaCAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACa                                                                                            >  1:288773/1‑148 (MQ=255)
                           tGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATg                                                                                                                                            <  2:989661/73‑1 (MQ=255)
                           tGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATg                                                                                                                                            >  1:989661/1‑73 (MQ=255)
                             aTAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTc                                                                                                                                  <  4:66117/81‑1 (MQ=255)
                             aTAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTc                                                                                                                                  >  3:66117/1‑81 (MQ=255)
                                      gACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTa                                                      <  2:288773/148‑1 (MQ=255)
                                              ttcattGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGAt                                                                                                                                          >  2:663062/1‑56 (MQ=255)
                                              ttcattGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGAt                                                                                                                                          <  3:433894/56‑1 (MQ=255)
                                              ttcattGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGAt                                                                                                                                          >  4:433894/1‑56 (MQ=255)
                                              ttcattGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGAt                                                                                                                                          <  1:663062/56‑1 (MQ=255)
                                               tcattGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTCAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACa                                                                                            <  4:427432/101‑1 (MQ=255)
                                               tcattGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTCAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACa                                                                                            >  3:427432/1‑101 (MQ=255)
                                                 attGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCt                                                                <  2:457827/127‑1 (MQ=255)
                                                 attGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCt                                                                >  1:457827/1‑127 (MQ=255)
                                                           ttAGCACACCAGGCCGGATGTGATCCGGCCTGATg                                                                                                                                                  >  2:65486/1‑35 (MQ=255)
                                                           ttAGCACACCAGGCCGGATGTGATCCGGCCTGATg                                                                                                                                                  <  1:65486/35‑1 (MQ=255)
                                                                   tcAGGCCGGATCACATCCGGCCTGGTGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTc                                                                                 <  4:10033/91‑1 (MQ=38)
                                                                   tcAGGCCGGATCACATCCGGCCTGGTGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTc                                                                                 >  3:10033/2‑92 (MQ=38)
                                                                   tcAGGCCGGATCACATCCGGCCTGGTGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATAc                                            >  3:463616/2‑129 (MQ=255)
                                                                   tcAGGCCGGATCACATCCGGCCTGGTGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATAc                                            <  4:463616/128‑1 (MQ=255)
                                                                   ccAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGaa                                                                                                                 >  4:138048/1‑60 (MQ=255)
                                                                   ccAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGaa                                                                                                                 <  3:138048/60‑1 (MQ=255)
                                                                      ggCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGaaa                                                                           >  3:254062/1‑95 (MQ=255)
                                                                      ggCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGaaa                                                                           <  4:254062/95‑1 (MQ=255)
                                                                                gATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATACCGCTGGAGTATcc            >  3:656386/1‑148 (MQ=255)
                                                                                 aTCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCAt                                              <  4:136080/113‑1 (MQ=255)
                                                                                 aTCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCAt                                              >  3:136080/1‑113 (MQ=255)
                                                                                  tCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTc                                                                     >  2:674514/1‑89 (MQ=255)
                                                                                  tCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTc                                                                     <  1:674514/89‑1 (MQ=255)
                                                                                  tCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCaa                                         <  2:188102/117‑1 (MQ=255)
                                                                                  tCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCaa                                         >  1:188102/1‑117 (MQ=255)
                                                                                   ccGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCAt                                              <  1:175556/111‑1 (MQ=255)
                                                                                   ccGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCAt                                              >  2:175556/1‑111 (MQ=255)
                                                                                       ccTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATACCGCTGGAGTATCCAGTGACa     <  4:656386/148‑1 (MQ=255)
                                                                                          gATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATACCGCTGGAGTATCCAGTGACAatc  >  3:244390/1‑148 (MQ=255)
                                                                                           |                                                                                                                                                  
AACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATACCGCTGGAGTATCCAGTGACAATC  >  NC_000913/2028080‑2028317

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A