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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,243,361 G→C 25.3% S79S (TCC→TCG)  nfi ← endonuclease V

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,243,3610GC25.3% 114.4 / 36.8 75S79S (TCC→TCG) nfiendonuclease V
Reads supporting (aligned to +/- strand):  ref base G (30/26);  new base C (7/12);  total (37/38)
Fisher's exact test for biased strand distribution p-value = 2.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 102 total aligned reads displayed.

CACTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACTTTATACTCGACCAGCTCAA  >  minE/2243298‑2243428
                                                               |                                                                   
cacTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaa                                                                 >  1:1936629/1‑68 (MQ=255)
cacTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaa                                                                 >  1:86394/1‑68 (MQ=255)
cacTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaa                                                                 >  1:2256003/1‑68 (MQ=255)
cacTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaa                                                                 >  1:1616602/1‑68 (MQ=255)
cacTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaa                                                                 >  1:2857870/1‑68 (MQ=255)
cacTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaa                                                                 >  1:1528565/1‑68 (MQ=255)
cacTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaa                                                                 >  1:1398142/1‑68 (MQ=255)
cacTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaa                                                                 >  1:3394295/1‑68 (MQ=255)
  cTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaagaa                                                              <  1:3429561/69‑1 (MQ=255)
   tAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaagaaa                                                             <  1:141143/69‑1 (MQ=255)
   tAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaagaaa                                                             <  1:1763671/69‑1 (MQ=255)
   tAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaagaaa                                                             <  1:1627794/69‑1 (MQ=255)
   tAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaagaaa                                                             <  1:354525/69‑1 (MQ=255)
   tAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGgaaagaaa                                                             <  1:771091/69‑1 (MQ=255)
    aaaTCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGaaaa                                                            <  1:3124673/69‑1 (MQ=255)
    aaaTCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGaaaa                                                            <  1:2991646/69‑1 (MQ=255)
         cGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTgg                                                       <  1:1244166/69‑1 (MQ=255)
         cGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTgg                                                       <  1:935128/69‑1 (MQ=255)
         cGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTgg                                                       <  1:1843749/69‑1 (MQ=255)
         cGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTgg                                                       <  1:2002916/69‑1 (MQ=255)
         cGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTgg                                                       <  1:819490/69‑1 (MQ=255)
         cGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTgg                                                       <  1:1496878/69‑1 (MQ=255)
                tGCGACAGCATCTCCCACGCTGGCAGCAGCGCAGGATATTCGCGGAACGAGAGAAAACCTGGAATga                                                  >  1:1123090/1‑66 (MQ=255)
                tGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAACGAGAGAAAACCTGGa                                                      >  1:2966221/1‑63 (MQ=255)
                tGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAACGAGAGAAAACCTGGAATGTaa                                                >  1:2659467/1‑69 (MQ=255)
                tGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAACGAGAGAAAACCTGGAATGTaa                                                >  1:529719/1‑69 (MQ=255)
                tGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAACGAGAGAAAACCTGGAATGTaa                                                >  1:2209524/1‑69 (MQ=255)
                tGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAACGAGAGAAAACCTGGAATGTa                                                 >  1:538758/1‑68 (MQ=255)
                tGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAACGAGAGAAAACCTGGAATGTa                                                 >  1:1299655/1‑68 (MQ=255)
                 gCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTaa                                                >  1:2513812/1‑68 (MQ=255)
                    aCAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGc                                             <  1:730011/68‑1 (MQ=255)
                    aCAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGc                                             <  1:246425/68‑1 (MQ=255)
                    aCAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGc                                             <  1:243499/68‑1 (MQ=255)
                            tcCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCAtggtggtg                                    >  1:3310036/1‑69 (MQ=255)
                            tcCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCAtggtggtg                                    >  1:123775/1‑69 (MQ=255)
                            tcCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCAtggtggtg                                    >  1:119796/1‑69 (MQ=255)
                            tcCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCAtggtggtg                                    >  1:3141978/1‑69 (MQ=255)
                            tcCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCAtggtggtg                                    >  1:312996/1‑69 (MQ=255)
                            tcCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCAtggtggtg                                    >  1:1390814/1‑69 (MQ=255)
                            tcCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCAtggtggtg                                    >  1:2940098/1‑69 (MQ=255)
                            tcCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCAtggtggtg                                    >  1:1017638/1‑69 (MQ=255)
                            tcCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCAtggtggt                                     >  1:577234/1‑68 (MQ=255)
                                aCGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATTTAAGGCATGGTGGTGGc                                  <  1:2190789/67‑1 (MQ=255)
                                aCGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGTTGGTGGc                                  <  1:1307035/67‑1 (MQ=255)
                                aCGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGc                                  <  1:2565047/67‑1 (MQ=255)
                                aCGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGc                                  <  1:1612675/67‑1 (MQ=255)
                                aCGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGc                                  <  1:1614723/67‑1 (MQ=255)
                                aCGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGc                                  <  1:2465507/67‑1 (MQ=255)
                                aCGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGc                                  <  1:1830667/67‑1 (MQ=255)
                                aCGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGc                                  <  1:1728075/67‑1 (MQ=255)
                                                 gtatatTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:924596/67‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:2368618/69‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:3150217/69‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:21098/69‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:2166118/69‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:1529554/69‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:1021366/69‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:1175364/69‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:741193/69‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:180056/69‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:2510698/69‑1 (MQ=255)
                                                 ggATATTCGCGGAACGAGAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCCACTTTATAc               <  1:1671435/69‑1 (MQ=255)
                                                    tatTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACTTTATACTc             >  1:668354/1‑68 (MQ=255)
                                                    tatTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACTTTATACTCg            >  1:427093/1‑69 (MQ=255)
                                                    tatTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACTTTATACTCg            <  1:2067110/69‑1 (MQ=255)
                                                      ttCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACTTTATACTCg            >  1:1379960/1‑67 (MQ=255)
                                                        cgcgGAAGGAAAGAAAACCTGGAATGTAAGGCAtggtgg                                      >  1:3142777/1‑39 (MQ=255)
                                                        cgcgGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACtt                    >  1:2256463/1‑57 (MQ=255)
                                                        cgcgGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACtt                    >  1:1080663/1‑57 (MQ=255)
                                                        cgcgGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACt                     >  1:1988426/1‑56 (MQ=255)
                                                        cgcgGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACt                     >  1:2060298/1‑56 (MQ=255)
                                                        cgcgGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACt                     >  1:2552605/1‑56 (MQ=255)
                                                        cgcgGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACTTTATACTCGACCa        >  1:702270/1‑69 (MQ=255)
                                                           ggaacgagAGAAAACCTGTAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:1432117/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGc                                  >  1:2328303/1‑40 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:927392/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:3064356/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:86216/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:366756/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:766647/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:1081218/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:3344626/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:2033694/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:2194046/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:233950/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:2451108/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:2731054/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:2748092/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:2823852/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:1545836/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:1912911/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:31165/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:3188578/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:327301/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:3298017/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGcca                       >  1:1242215/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGAGGGcca                       >  1:3083857/1‑49 (MQ=255)
                                                           ggaacgagAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATCCGGGcc                        >  1:1019935/1‑49 (MQ=255)
                                                              aggaaAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACTTTATACTCGACCAGCTCaa  >  1:502029/1‑69 (MQ=255)
                                                              aggaaAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACTTTATACTCGACCAGCTCaa  >  1:2095189/1‑69 (MQ=255)
                                                               |                                                                   
CACTAAATCCGGCTTTTGCGACAGCATCTCCCACGCTGCCAGCAGCGCAGGATATTCGCGGAAGGAAAGAAAACCTGGAATGTAAGGCATGGTGGTGGCGATGCGGGCAACTTTATACTCGACCAGCTCAA  >  minE/2243298‑2243428

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A