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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,176,396 C→T 35.6% M6I (ATG→ATA)  gatC ← galactitol‑specific enzyme IIC component of PTS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,176,3960CT35.6% 76.8 / 72.1 73M6I (ATG→ATA) gatCgalactitol‑specific enzyme IIC component of PTS
Reads supporting (aligned to +/- strand):  ref base C (19/28);  new base T (11/15);  total (30/43)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.17e-01

ATATTTTAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTGTAATGCTTCGATACCGA  >  W3110S.gb/2176329‑2176466
                                                                   |                                                                      
atatTTTAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCAt                                                                      <  1:1912960/70‑1 (MQ=255)
atatTTTAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCAt                                                                      <  1:121350/70‑1 (MQ=255)
atatTTTAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCAt                                                                      >  1:1658028/1‑70 (MQ=255)
 tatTTTAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGa                                                                    >  1:932376/1‑71 (MQ=255)
    tttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACtt                                                                 >  1:4198209/1‑71 (MQ=255)
    tttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACtt                                                                 >  1:4138633/1‑71 (MQ=255)
    tttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACtt                                                                 >  1:4683618/1‑71 (MQ=255)
     ttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGc                                                                        >  1:1716923/1‑63 (MQ=255)
     ttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACTTc                                                                >  1:2996894/1‑71 (MQ=255)
     ttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACTTc                                                                >  1:830954/1‑71 (MQ=255)
     ttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGa                                                                    >  1:4124433/1‑67 (MQ=255)
     ttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACtt                                                                 <  1:283355/70‑1 (MQ=255)
     ttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACtt                                                                 <  1:1684183/70‑1 (MQ=255)
     ttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTc                                                                >  1:3717833/1‑71 (MQ=255)
     ttAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTc                                                                >  1:2214610/1‑71 (MQ=255)
             aataatGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACa                                                        <  1:3491017/71‑1 (MQ=255)
             aataatGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACa                                                        <  1:3701724/71‑1 (MQ=255)
             aataatGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACa                                                        <  1:454736/71‑1 (MQ=255)
             aataatGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCAt                                                                      <  1:2786486/57‑1 (MQ=255)
             aataatGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACa                                                        <  1:3472036/71‑1 (MQ=255)
             aataatGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACa                                                        <  1:410335/71‑1 (MQ=255)
             aataatGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACa                                                        <  1:4945574/71‑1 (MQ=255)
              ataatGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACAt                                                       <  1:1039720/71‑1 (MQ=255)
               taatGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATg                                                                     <  1:763020/56‑1 (MQ=255)
                    atgaCAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTc                                                  <  1:2890866/70‑1 (MQ=255)
                             ggCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACATAGGTCACCCCTGTa                                         <  1:503983/70‑1 (MQ=255)
                             ggCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACATAGGTCACCCCTGTa                                         <  1:3611034/70‑1 (MQ=255)
                             ggCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTaa                                        <  1:3368438/71‑1 (MQ=255)
                             ggCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTaa                                        <  1:3848716/71‑1 (MQ=255)
                             ggCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTaa                                        <  1:1474040/71‑1 (MQ=255)
                             ggCAGCAACACCGTAGGGCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACATAGGTCAccc                                              >  1:2618521/1‑65 (MQ=255)
                                 gcaTCACCGTAGGGCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACAt                                                       >  1:1379374/1‑52 (MQ=255)
                                 gcaTCACCGTAGGGCCGAGGTCGAGAATATAACGCAt                                                                      <  1:1104367/37‑1 (MQ=255)
                                    tCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTa                                         <  1:2661938/63‑1 (MQ=255)
                                    tCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTa                                         <  1:3939693/63‑1 (MQ=255)
                                     cACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGt                                  >  1:4202570/1‑69 (MQ=255)
                                      aCCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGt                                  >  1:4566554/1‑68 (MQ=255)
                                      aCCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAg                               <  1:1770363/71‑1 (MQ=255)
                                      aCCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAg                               <  1:1447794/71‑1 (MQ=255)
                                       ccGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAg                               >  1:3002486/1‑70 (MQ=255)
                                        cGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAgg                                                    >  1:4933566/1‑48 (MQ=255)
                                        cGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAgg                                                    >  1:1802229/1‑48 (MQ=255)
                                        cGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAgg                                                    >  1:4160581/1‑48 (MQ=255)
                                            gggCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattt                          >  1:2743879/1‑70 (MQ=255)
                                             ggCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAatttt                         <  1:1396727/70‑1 (MQ=255)
                                             ggCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAatttta                        <  1:2579898/71‑1 (MQ=255)
                                              gCCGAGGTCGAGAATATAACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGa                              <  1:1572020/64‑1 (MQ=255)
                                               ccGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCAcccc                                             <  1:84203/48‑1 (MQ=255)
                                                 gAGGTCGAGAATATAACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattttatttt                    <  1:1922480/71‑1 (MQ=255)
                                                 gAGGTCGAGAATATAACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattttatttt                    <  1:4599358/71‑1 (MQ=255)
                                                  aGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTg                   <  1:1103960/71‑1 (MQ=255)
                                                   ggTCGAGAATATAACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTGt                  <  1:578080/71‑1 (MQ=255)
                                                   ggTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTg                   <  1:2065154/70‑1 (MQ=255)
                                                   ggTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTCTAAGATAGTCAGAATTTTATTTTGt                  <  1:4292732/71‑1 (MQ=255)
                                                    gTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTg                   >  1:758058/1‑69 (MQ=255)
                                                     tCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGa                                      <  1:4614249/49‑1 (MQ=255)
                                                         gaATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattt                          >  1:2123936/1‑57 (MQ=255)
                                                         gaATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattt                          >  1:2364001/1‑57 (MQ=255)
                                                         gaATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTGTAATGCt            <  1:2393231/71‑1 (MQ=255)
                                                          aaTATAACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattt                          <  1:4378243/56‑1 (MQ=255)
                                                          aaTATAACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattt                          <  1:1798979/56‑1 (MQ=255)
                                                           atatAACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattt                          <  1:2567630/55‑1 (MQ=255)
                                                           atatAACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTGTAATGCTTc          <  1:2365397/71‑1 (MQ=255)
                                                            tataACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAatttta                        <  1:4295962/56‑1 (MQ=255)
                                                            tataACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAatttta                        <  1:1426107/56‑1 (MQ=255)
                                                             ataACGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTGTAATGCTTcga        >  1:4643712/1‑71 (MQ=255)
                                                              taACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAg                                   >  1:1067475/1‑43 (MQ=255)
                                                              taACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattttatt                      >  1:4623516/1‑56 (MQ=255)
                                                              taACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattttatt                      >  1:2362114/1‑56 (MQ=255)
                                                              taACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAattttat                       >  1:3381206/1‑55 (MQ=255)
                                                               aaCGTATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTGTAATGCt            >  1:1961787/1‑65 (MQ=255)
                                                                aCGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTGTaa                >  1:91064/1‑60 (MQ=255)
                                                                aCGCATGACTTCTGAAAACATAGGTCACCACTGTAAGATAGTCAGAATTTTATTTTGTAATGCTTcgatac     >  1:551769/1‑71 (MQ=255)
                                                                  gCATGACTTCTGAAAACATAGCTCACCCCTGTAAGATAGTCAGAATTTTATTTTGt                  <  1:3728709/56‑1 (MQ=255)
                                                                   cATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTGTAATGCTTcgataccga  >  1:2687692/1‑71 (MQ=255)
                                                                   |                                                                      
ATATTTTAGAAAAAATAATGATGACAATCGGCAGCATCACCGTAGGGCCGAGGTCGAGAATATAACGCATGACTTCTGAAAACATAGGTCACCCCTGTAAGATAGTCAGAATTTTATTTTGTAATGCTTCGATACCGA  >  W3110S.gb/2176329‑2176466

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