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
A1 F3 I0 R2 260 44.3 3360226 90.5% 3041004 64.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,005,355 G→A 22.3% K146K (AAG→AAA)  ygeW → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,005,3550GA22.3% 172.0 / 44.1 85K146K (AAG→AAA) ygeWconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (48/18);  new base A (11/8);  total (59/26)
Fisher's exact test for biased strand distribution p-value = 2.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCACCCGACTCAGTC  >  W3110S.gb/3005309‑3005423
                                              |                                                                    
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGgtg                                                               >  1:591967/1‑54 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:1020514/1‑56 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:1094081/1‑56 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:2775825/1‑56 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:2837694/1‑56 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:1897058/1‑56 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:1805116/1‑56 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:3127750/1‑56 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:949437/1‑56 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:3134040/1‑56 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:346738/1‑56 (MQ=255)
aCGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTa                                                             >  1:571562/1‑56 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:216598/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:2549067/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:3180945/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:1014968/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:1537441/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:1085140/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:381342/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:730640/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:2760531/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:1126347/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:97394/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:1311454/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:301911/1‑71 (MQ=255)
  gCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGc                                            >  1:1244010/1‑71 (MQ=255)
       tatGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:1530421/1‑71 (MQ=255)
       tatGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:2055463/1‑71 (MQ=255)
       tatGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:962137/1‑71 (MQ=255)
       tatGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:1814957/1‑71 (MQ=255)
       tatGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:579348/1‑71 (MQ=255)
         tGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:1662424/1‑69 (MQ=255)
         tGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGt                                      >  1:2967888/1‑70 (MQ=255)
         tGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGt                                      <  1:871973/70‑1 (MQ=255)
         tGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGt                                      >  1:861489/1‑70 (MQ=255)
         tGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGt                                      >  1:3251476/1‑70 (MQ=255)
         tGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGt                                      >  1:455551/1‑70 (MQ=255)
         tGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGt                                      >  1:2480912/1‑70 (MQ=255)
         tGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGt                                      >  1:1633517/1‑70 (MQ=255)
         tGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGt                                      >  1:147025/1‑70 (MQ=255)
         tGCGTGAAGTTGGCGCTGCACTTGATCACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGt                                      >  1:2121551/1‑70 (MQ=255)
           cGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGaa                                   >  1:1926392/1‑71 (MQ=255)
           cGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGaa                                   >  1:548244/1‑71 (MQ=255)
           cGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGaa                                   >  1:1771645/1‑71 (MQ=255)
           cGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGaa                                   >  1:2882009/1‑71 (MQ=255)
           cGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGaa                                   >  1:1169902/1‑71 (MQ=255)
           cGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGaa                                   >  1:1237926/1‑71 (MQ=255)
           cGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGaa                                   >  1:2604732/1‑71 (MQ=255)
                aGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCtcc                              <  1:696383/71‑3 (MQ=255)
                aGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGc                              <  1:638900/71‑1 (MQ=255)
                aGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGc                              <  1:349816/71‑1 (MQ=255)
                aGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGc                              <  1:3211420/71‑1 (MQ=255)
                aGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGc                              <  1:1515071/71‑1 (MQ=255)
                aGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGc                              <  1:1685133/71‑1 (MQ=255)
                aGTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGc                              <  1:1456292/71‑1 (MQ=255)
                 gTTGGCGCTGCACTTGATGACGGTTACAAACAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGc                              <  1:2076243/70‑1 (MQ=255)
                       gcTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGa                       <  1:3236733/71‑1 (MQ=255)
                       gcTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGa                       <  1:1545606/71‑1 (MQ=255)
                       gcTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGa                       <  1:1333075/71‑1 (MQ=255)
                        cTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCTGCttt                                         <  1:1936452/52‑1 (MQ=255)
                        cTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCttt                                         <  1:927506/52‑1 (MQ=255)
                        cTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCttt                                         <  1:943564/52‑1 (MQ=255)
                        cTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCttt                                         <  1:2192067/52‑1 (MQ=255)
                        cTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCttt                                         <  1:88533/52‑1 (MQ=255)
                        cTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCttt                                         <  1:1760536/52‑1 (MQ=255)
                        cTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATTCGa                       <  1:1736159/70‑1 (MQ=255)
                          gCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:2183365/1‑52 (MQ=255)
                          gCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:1514260/1‑52 (MQ=255)
                          gCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:971125/1‑52 (MQ=255)
                          gCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:2963110/1‑52 (MQ=255)
                          gCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAg                                       >  1:2112147/1‑52 (MQ=255)
                          gCACTTAATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCgg                                             >  1:430169/1‑46 (MQ=255)
                                    aCGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCAccc           >  1:992577/1‑70 (MQ=255)
                                    aCGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCAccc           >  1:1543066/1‑70 (MQ=255)
                                      ggTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCACCCGAc        >  1:2143621/1‑71 (MQ=255)
                                          aCAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCaa                            >  1:811682/1‑47 (MQ=255)
                                          aCAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCaa                            >  1:76239/1‑47 (MQ=255)
                                          aCAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCaa                            >  1:153801/1‑47 (MQ=255)
                                            aaGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCACCCGACTCAGTc  <  1:139873/71‑1 (MQ=255)
                                            aaGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCACCCGACTCAGTc  <  1:2486192/71‑1 (MQ=255)
                                            aaGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCACCCGACTCAGTc  <  1:241940/71‑1 (MQ=255)
                                            aaGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCACCCGACTCAGTc  <  1:1316555/71‑1 (MQ=255)
                                            aaGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCACCCGACTCAGTc  <  1:2242531/71‑1 (MQ=255)
                                            aaGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCACCCGACTCAGTc  <  1:3134349/71‑1 (MQ=255)
                                            aaGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCACCCGACTCAGTc  <  1:3210640/71‑1 (MQ=255)
                                              |                                                                    
ACGCCTATATGCGTGAAGTTGGCGCTGCACTTGATGACGGTTACAAGCAGGGTGTACTGCCACAGCGTCCGGCTTTAGTGAACCTGCAATGCGATATTGACCACCCGACTCAGTC  >  W3110S.gb/3005309‑3005423

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