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 1,698,852 T→C 25.8% H244H (CAT→CAC)  csiE → stationary phase inducible protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,698,8520TC25.8% 91.5 / 29.9 81H244H (CAT→CAC) csiEstationary phase inducible protein
Reads supporting (aligned to +/- strand):  ref base T (44/16);  new base C (8/13);  total (52/29)
Fisher's exact test for biased strand distribution p-value = 7.19e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGCTTTAT  >  minE/1698799‑1698912
                                                     |                                                            
gcgcATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGa                                               <  1:2403806/69‑1 (MQ=255)
gcgcATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGa                                               <  1:1289964/69‑1 (MQ=255)
       aGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTc                                        >  1:1308195/1‑69 (MQ=255)
             acagacaATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGttttt                                  <  1:3394040/69‑1 (MQ=255)
                     ttGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGaa                          <  1:2447079/69‑1 (MQ=255)
                     ttGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGaa                          <  1:2056426/69‑1 (MQ=255)
                      tGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAAc                         >  1:1988452/1‑69 (MQ=255)
                                tATCAAGCGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:638692/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:2123684/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:2322650/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:2404719/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:2221963/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:2225891/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:2745348/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:2272141/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:1827207/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:179701/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:164022/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:3151441/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:1563832/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:3327814/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:488208/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:1326724/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:342130/1‑68 (MQ=255)
                                tATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt                >  1:3395384/1‑68 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAAt                                            >  1:1226191/1‑38 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATg                                           >  1:302266/1‑39 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatgatg                            >  1:2623810/1‑54 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatgatg                            >  1:2727930/1‑54 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatgatg                            >  1:1463928/1‑54 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatgatg                            >  1:1499034/1‑54 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatgatg                            >  1:467280/1‑54 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatgatg                            >  1:2819646/1‑54 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatgatg                            >  1:2232052/1‑54 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:346402/1‑69 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:283197/1‑69 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:558173/1‑69 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:958360/1‑69 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:2137232/1‑69 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:1272190/1‑69 (MQ=255)
                                  tCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:1520079/1‑69 (MQ=255)
                                   cAAACGTCTGTTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgcg             >  1:1502953/1‑66 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:161522/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:891424/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:1490391/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:3302381/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:3215422/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:1696594/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:2981182/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:2774439/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:2752728/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:1897609/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:2450582/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:1963626/50‑1 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgcg             >  1:756298/1‑66 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgcg             >  1:1063544/1‑66 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgcg             >  1:1178063/1‑66 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgcg             >  1:426465/1‑66 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgcg             >  1:2485641/1‑66 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgcg             >  1:3181379/1‑66 (MQ=255)
                                   cAAACGTCTGGTAAACCACTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgcg             >  1:318834/1‑66 (MQ=255)
                                    aaaCGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:277874/1‑67 (MQ=255)
                                    aaaCGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:844705/1‑67 (MQ=255)
                                    aaaCGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:2263353/1‑67 (MQ=255)
                                    aaaCGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:2770423/1‑67 (MQ=255)
                                    aaaCGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             >  1:1956301/1‑67 (MQ=255)
                                      aCGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCa         >  1:3302794/1‑69 (MQ=255)
                                      aCGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCa         >  1:1862908/1‑69 (MQ=255)
                                           tGGTAAACCACTTTCTTGAGCTGGGAAATGTTCGTTTTTatg                               <  1:3139674/42‑1 (MQ=38)
                                               aaaCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             <  1:2048100/56‑1 (MQ=255)
                                               aaaCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             <  1:2052062/56‑1 (MQ=255)
                                               aaaCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             <  1:1147625/56‑1 (MQ=255)
                                               aaaCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             <  1:1856773/56‑1 (MQ=255)
                                               aaaCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             <  1:418915/56‑1 (MQ=255)
                                               aaaCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             <  1:1310040/56‑1 (MQ=255)
                                               aaaCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             <  1:1473164/56‑1 (MQ=255)
                                               aaaCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGCTTtat  <  1:579108/67‑1 (MQ=255)
                                               aaaCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGCTTtat  <  1:1999432/67‑1 (MQ=255)
                                               aaaCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGCTTta   <  1:1062286/66‑1 (MQ=255)
                                                 aCCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtgtg             <  1:2958847/54‑1 (MQ=255)
                                                  ccATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGCtt     >  1:2830975/1‑61 (MQ=255)
                                                     |                                                            
GCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGCTTTAT  >  minE/1698799‑1698912

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