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
A5 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,113,649 C→T 16.7% A1374T (GCA→ACA)  yghJ ← predicted inner membrane lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,113,6490CT16.7% 183.1 / 25.3 72A1374T (GCA→ACA) yghJpredicted inner membrane lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (35/25);  new base T (7/5);  total (42/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

GCAGAGGAGTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTCTCCTCCAGATATT  >  W3110S.gb/3113580‑3113717
                                                                     |                                                                    
gCAGAGGAGTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCACATTCCTTCAGCTGTGCg                                                                     >  1:2905597/1‑71 (MQ=255)
 cAGAGGAGTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCg                                                                     <  1:3375777/70‑1 (MQ=255)
  agagGAGTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTa                                                                   >  1:1498157/1‑71 (MQ=255)
    aggagTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACa                                                                 >  1:2047920/1‑71 (MQ=255)
    aggagTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACa                                                                 <  1:1954324/71‑1 (MQ=255)
        gTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATcag                                                             >  1:1191940/1‑71 (MQ=255)
        gTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATcag                                                             >  1:1445332/1‑71 (MQ=255)
           ccATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGc                                                                      >  1:4614842/1‑59 (MQ=255)
           ccATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATcag                                                             >  1:997802/1‑68 (MQ=255)
               cTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACgg                                                      >  1:3695515/1‑71 (MQ=255)
               cTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACgg                                                      >  1:1506836/1‑71 (MQ=255)
               cTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGa                                                         >  1:2230484/1‑68 (MQ=255)
               cTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACgg                                                      >  1:3988970/1‑71 (MQ=255)
                tGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCTTACATCAGCAGACg                                                       >  1:4502752/1‑69 (MQ=255)
                tGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACAt                                                                >  1:617664/1‑60 (MQ=255)
                tGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGt                                                     >  1:3251542/1‑71 (MQ=255)
                  gATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGTTTACa                                                                 <  1:1821009/57‑1 (MQ=255)
                  gATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACg                                                       <  1:1307161/67‑1 (MQ=255)
                  gATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTc                                                    <  1:880244/70‑1 (MQ=255)
                  gATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTc                                                    <  1:393875/70‑1 (MQ=255)
                    tACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCAcc                                                 >  1:1721951/1‑71 (MQ=255)
                       cATTTCTTGATATCAAAGTTTTTATCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCg                                               >  1:2665345/1‑70 (MQ=255)
                         tttCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGt                                                                    <  1:3390723/47‑1 (MQ=255)
                         tttCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCAc                                            >  1:3737035/1‑71 (MQ=255)
                         tttCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCAc                                            <  1:1272549/71‑1 (MQ=255)
                         tttCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCAc                                            >  1:2426643/1‑71 (MQ=255)
                           tCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCAc                                            >  1:980255/1‑69 (MQ=255)
                            cTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCg                                                                     >  1:409542/1‑43 (MQ=255)
                             ttGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCAccgcc                                        >  1:626066/1‑71 (MQ=255)
                                atatCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATcagc                                                            >  1:95295/1‑48 (MQ=255)
                                  atCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTg                                   >  1:241434/1‑71 (MQ=255)
                                   tCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGc                                  <  1:4354575/71‑1 (MQ=255)
                                     aaaGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGa                                                         >  1:1177266/1‑46 (MQ=255)
                                     aaaGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                                 <  1:4254296/70‑1 (MQ=255)
                                     aaaGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                                 <  1:985252/70‑1 (MQ=255)
                                       aGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGt                                                     <  1:1631508/48‑1 (MQ=255)
                                       aGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCAt                              >  1:1834696/1‑71 (MQ=255)
                                       aGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCAt                              >  1:3487938/1‑71 (MQ=255)
                                        gTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATg                             >  1:4227742/1‑71 (MQ=255)
                                        gTTTTTCTCTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATg                             >  1:4277535/1‑71 (MQ=255)
                                        gTTTTTCTCTGCCCATTCCTTCAGCTGTGTCTACAt                                                                <  1:296354/36‑1 (MQ=37)
                                        gTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATg                             >  1:4359195/1‑71 (MQ=255)
                                         tttttCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGAc                                                        <  1:1437238/43‑1 (MQ=255)
                                         tttttCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGAc                                                        <  1:1837709/43‑1 (MQ=255)
                                          ttttCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGt                                    >  1:2318672/1‑62 (MQ=255)
                                           tttCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACgg                                                      >  1:4567437/1‑43 (MQ=255)
                                           tttCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGcc                           <  1:3647795/70‑1 (MQ=255)
                                           tttCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCt                          >  1:2907438/1‑71 (MQ=255)
                                            ttCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGTAGACGGTCACCCGCACCGCCGCGTGCCCATGCCt                          <  1:413973/70‑1 (MQ=255)
                                            ttCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGcc                           <  1:1250667/69‑1 (MQ=255)
                                             tctcTGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCAccc                                                >  1:3008595/1‑47 (MQ=255)
                                             tctcTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTgg                        >  1:3546061/1‑71 (MQ=255)
                                              ctctGCCCATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGc                            <  1:1252056/66‑1 (MQ=255)
                                              ctctGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCt                          <  1:4560170/68‑1 (MQ=255)
                                              ctctGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTgg                        <  1:2379456/70‑1 (MQ=255)
                                                 tGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACcgccgc                                      >  1:842242/1‑53 (MQ=255)
                                                 tGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGcc                                 >  1:1031107/1‑58 (MQ=255)
                                                 tGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGgttgt                    >  1:668957/1‑71 (MQ=255)
                                                 tGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGgtt                      <  1:279003/69‑1 (MQ=255)
                                                   cccATTCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCAAGCCTGGttgttg                  >  1:1227662/1‑71 (MQ=255)
                                                   cccATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGgttgttc                  >  1:2642793/1‑70 (MQ=255)
                                                   cccATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGgttgt                    <  1:3896960/69‑1 (MQ=255)
                                                    ccATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGc                 >  1:4279999/1‑71 (MQ=255)
                                                    ccATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGc                 <  1:882298/71‑1 (MQ=255)
                                                     cATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGgttgt                    >  1:4379268/1‑67 (MQ=255)
                                                       ttCCTTCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGgttgt                    <  1:1621546/65‑1 (MQ=255)
                                                          cTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGctct              >  1:1347184/1‑68 (MQ=255)
                                                            tCAGCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTctcctc          >  1:1562415/1‑70 (MQ=255)
                                                               gCTGTGTGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTCTCCTCCa        <  1:2714523/69‑1 (MQ=255)
                                                                cTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTCTCCTCCAGa      <  1:1191309/70‑1 (MQ=255)
                                                                  gtgCGTACATCAGCAGACGGTCACCCGAACCGCCGCGTGCCCATGCCt                          <  1:3651261/48‑1 (MQ=255)
                                                                   tgCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTCTCCTCCAGatat   <  1:1084988/70‑1 (MQ=255)
                                                                   tgCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTCTCCTCCAGATAtt  <  1:1867550/71‑1 (MQ=255)
                                                                     cGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGgttgt                    >  1:239964/1‑51 (MQ=255)
                                                                     |                                                                    
GCAGAGGAGTGCCATCTGGATACCATTTCTTGATATCAAAGTTTTTCTCTGCCCATTCCTTCAGCTGTGCGTACATCAGCAGACGGTCACCCGCACCGCCGCGTGCCCATGCCTGGTTGTTGCTCTCCTCCAGATATT  >  W3110S.gb/3113580‑3113717

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