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 1,768,173 C→T 65.9% A175A (GCG→GCA)  rluD ← 23S rRNA pseudouridine synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,768,1730CT65.9% 60.0 / 47.3 85A175A (GCG→GCA) rluD23S rRNA pseudouridine synthase
Reads supporting (aligned to +/- strand):  ref base C (14/15);  new base T (25/31);  total (39/46)
Fisher's exact test for biased strand distribution p-value = 8.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

TGGGTACGTTTGGTCGGGTGGCGACTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGT  >  minE/1768105‑1768232
                                                                    |                                                           
tGGGTACGTTTGGTCGGGTGGCGACTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGACCAATc                                                             >  1:1287771/1‑69 (MQ=255)
tGGGTACGTTTGGTCGGGTGGCGACTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGACCAATc                                                             >  1:629923/1‑69 (MQ=255)
tGGGTACGTTTGGTCGGGTGGCGACTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGACCAATc                                                             >  1:61062/1‑69 (MQ=255)
  ggTACGTTTGGTCGGGTGGCGACTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGACCAATCGc                                                           <  1:819695/69‑1 (MQ=255)
  ggTACGTTTGGTCGGGTGGCGACTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGACCAATCGc                                                           <  1:23200/69‑1 (MQ=255)
    tACGTTTGGTCGGGTGGCGATTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGACCAATCGCCa                                                         >  1:2790702/1‑69 (MQ=255)
    tACGTTTGGTCGGGTGGCGACTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGCCCAATCGCCa                                                         >  1:1847066/1‑69 (MQ=255)
    tACGTTTGGTCGGGTGGCGACTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGACCAATCGCCa                                                         >  1:2144404/1‑69 (MQ=255)
    tACGTTTGGTCGGGTGGCGACTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGACCAATCGCCa                                                         >  1:1979440/1‑69 (MQ=255)
                                            gCCACCTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGa                 <  1:2498227/69‑1 (MQ=255)
                                            gCCACCTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGa                 <  1:2834303/69‑1 (MQ=255)
                                            gCCACCTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGa                 <  1:3259631/69‑1 (MQ=255)
                                            gCCACCTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGa                 <  1:1003238/69‑1 (MQ=255)
                                             ccACCTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGa                 <  1:1227179/68‑1 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGCTTc              >  1:3306862/4‑68 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTc              >  1:3379440/4‑68 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTc              >  1:3424988/4‑68 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTc              >  1:301875/4‑68 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTc              >  1:2243943/4‑68 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTc              >  1:115186/4‑68 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTc              >  1:793645/4‑68 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:2389606/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:2274237/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:2342248/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:2231495/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:2482267/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:2487376/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:2695884/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:2943924/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:3191238/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:3329477/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:653778/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:781877/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:971338/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:1107087/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:1474964/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:1311547/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             >  1:2076159/4‑69 (MQ=255)
                                                ccagCGGTCATATGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCAAGCCGTTGCAAAGATTc              >  1:147322/4‑68 (MQ=255)
                                                ccTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             <  1:2140358/69‑1 (MQ=255)
                                                ccTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             <  1:2090995/69‑1 (MQ=255)
                                                ccTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             <  1:1893371/69‑1 (MQ=255)
                                                ccTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             <  1:1886796/69‑1 (MQ=255)
                                                ccTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             <  1:1215121/69‑1 (MQ=255)
                                                ccTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             <  1:6156/69‑1 (MQ=255)
                                                ccTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             <  1:2587551/69‑1 (MQ=255)
                                                ccTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCg             <  1:1354248/69‑1 (MQ=255)
                                                        cATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAAcg     >  1:1531778/1‑69 (MQ=255)
                                                        cATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAAcg     >  1:39991/1‑69 (MQ=255)
                                                         atatGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAAcgc    >  1:2938156/1‑69 (MQ=255)
                                                         atatGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAAcgc    >  1:1511316/1‑69 (MQ=255)
                                                         atatGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAAcgc    >  1:1436044/1‑69 (MQ=255)
                                                         atatGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAAcgc    >  1:2341522/1‑69 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACTCGt  <  1:1149753/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:473708/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:2217585/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:1142126/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:3158584/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:1720649/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:2900512/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:2179505/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:1738274/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:1731050/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:275851/69‑1 (MQ=255)
                                                           atGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:2761122/69‑1 (MQ=255)
                                                           atGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  >  1:2899021/1‑69 (MQ=255)
                                                           atGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  >  1:2632805/1‑69 (MQ=255)
                                                           atGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  >  1:2767607/1‑69 (MQ=255)
                                                           atGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  >  1:151610/1‑69 (MQ=255)
                                                            tGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:2702764/68‑1 (MQ=255)
                                                            tGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:236022/68‑1 (MQ=255)
                                                            tGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:373748/68‑1 (MQ=255)
                                                            tGACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:2660945/68‑1 (MQ=255)
                                                             gACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:545772/67‑1 (MQ=255)
                                                             gACCAATTGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGt  <  1:3063353/67‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:1727285/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:480809/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:487705/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:3287145/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:1760825/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:1819499/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:1294787/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:182322/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:1175507/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:2157350/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:897459/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:94321/36‑1 (MQ=255)
                                                              aCCAATTGCCACCGCTTCATACTCACGAGTAATTTc                                <  1:2982182/36‑1 (MQ=255)
                                                                    |                                                           
TGGGTACGTTTGGTCGGGTGGCGACTGATTGGCTCGTCCACCGTGCCACCTGCGGTCATATGACCAATCGCCACCGCTTCATACTCACGAGTAATTTCACGCCGTTGCAAAGATTCGACTAAACGCGT  >  minE/1768105‑1768232

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A