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 626,245 C→T 30.8% A53V (GCC→GTC)  ycaQ → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE626,2450CT30.8% 78.8 / 39.0 84A53V (GCC→GTC) ycaQconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (41/17);  new base T (21/5);  total (62/22)
Fisher's exact test for biased strand distribution p-value = 4.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

GGAGGATATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTC  >  minE/626180‑626311
                                                                 |                                                                  
ggaggaTATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCg                                                                 <  1:1995688/69‑1 (MQ=255)
ggaggaTATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCg                                                                 <  1:1933727/69‑1 (MQ=255)
ggaggaTATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCg                                                                 <  1:1918387/69‑1 (MQ=255)
ggaggaTATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCg                                                                 <  1:1219705/69‑1 (MQ=255)
ggaggaTATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCg                                                                 <  1:2193655/69‑1 (MQ=255)
ggaggaTATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCg                                                                 <  1:766844/69‑1 (MQ=255)
ggaggaTATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCg                                                                 <  1:1373009/69‑1 (MQ=255)
ggaggaTATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCg                                                                 <  1:2490590/69‑1 (MQ=255)
ggaggaTATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCg                                                                 <  1:1480974/69‑1 (MQ=255)
ggaggaTATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCg                                                                 <  1:549867/69‑1 (MQ=255)
               aaCGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCata                                                        >  1:3061850/1‑63 (MQ=255)
               aaCGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCata                                                        >  1:2045079/1‑63 (MQ=255)
               aaCGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCata                                                        >  1:3321397/1‑63 (MQ=255)
               aaCGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCata                                                        >  1:1669969/1‑63 (MQ=255)
               aaCGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCata                                                        >  1:2369220/1‑63 (MQ=255)
               aaCGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCata                                                        >  1:1580546/1‑63 (MQ=255)
               aaCGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCata                                                        >  1:814954/1‑63 (MQ=255)
               aaCGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCata                                                        >  1:1136334/1‑63 (MQ=255)
               aaCGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCata                                                        >  1:1110899/1‑63 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:436497/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:2471243/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:3182070/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:1004560/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:3319018/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:298074/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:2915016/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:2808785/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:1452750/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:984983/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:889318/1‑67 (MQ=255)
                     ctcCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCtt                                              >  1:1624778/1‑67 (MQ=255)
                             tGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAgtcgtc                                    >  1:3257880/1‑69 (MQ=255)
                             tGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAgtcgtc                                    >  1:133103/1‑69 (MQ=255)
                             tGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAgtcgt                                     >  1:564396/1‑68 (MQ=255)
                               tCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCt                                   >  1:3436353/1‑68 (MQ=255)
                               tCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCt                                   >  1:966354/1‑68 (MQ=255)
                               tCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCt                                   >  1:2862215/1‑68 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAgccg                                      >  1:1685817/1‑55 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTAt                         >  1:1746876/1‑68 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:484176/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:516147/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:3362860/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:594451/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:3017598/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:2997019/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:3420740/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:2577171/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:2738872/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:1093865/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:131070/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:1393987/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:1523200/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:1731285/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:2307125/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:2237045/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:1819781/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        >  1:2234190/1‑69 (MQ=255)
                                         aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTCTCAGCCGTCTGGGAGATTATc                        >  1:2102096/1‑69 (MQ=255)
                                          aaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGTGAGATTATc                        <  1:3004942/68‑1 (MQ=255)
                                          aaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        <  1:885545/68‑1 (MQ=255)
                                          aaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        <  1:2498651/68‑1 (MQ=255)
                                          aaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        <  1:533575/68‑1 (MQ=255)
                                          aaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc                        <  1:5181/68‑1 (MQ=255)
                                            tCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTg                     >  1:867053/1‑69 (MQ=255)
                                            tCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTg                     >  1:3360344/1‑69 (MQ=255)
                                            tCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTg                     >  1:1427952/1‑69 (MQ=255)
                                                       aaTATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTg          >  1:2216587/1‑69 (MQ=255)
                                                       aaTATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTg          >  1:757102/1‑69 (MQ=255)
                                                       aaTATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTg          >  1:3272872/1‑69 (MQ=255)
                                                       aaTATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTg          >  1:349397/1‑69 (MQ=255)
                                                           ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg      >  1:1653515/1‑69 (MQ=255)
                                                           ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg      >  1:2808472/1‑69 (MQ=255)
                                                           ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg      >  1:3324505/1‑69 (MQ=255)
                                                           ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg      >  1:3293259/1‑69 (MQ=255)
                                                           ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg      >  1:1306717/1‑69 (MQ=255)
                                                           ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg      >  1:2730976/1‑69 (MQ=255)
                                                           ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg      >  1:1066277/1‑69 (MQ=255)
                                                             gttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGa     <  1:1999733/68‑1 (MQ=255)
                                                             gttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGa     <  1:2149632/68‑1 (MQ=255)
                                                             gttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGa     <  1:2574915/68‑1 (MQ=255)
                                                                gCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGtc  <  1:2382793/68‑1 (MQ=255)
                                                                gCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGtc  <  1:3352669/68‑1 (MQ=255)
                                                                gCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGtc  <  1:3325009/68‑1 (MQ=255)
                                                                gCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGtc  <  1:1357729/68‑1 (MQ=255)
                                                                 |                                                                  
GGAGGATATTCCGGCAACGATCTCCCGCATGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTC  >  minE/626180‑626311

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A