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 1,170,030 C→T 41.9% intergenic (‑204/‑32) ynjH ← / → gdhA hypothetical protein/glutamate dehydrogenase, NADP‑specific

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,170,0300CT41.9% 45.4 / 83.5 115intergenic (‑204/‑32)ynjH/gdhAhypothetical protein/glutamate dehydrogenase, NADP‑specific
Reads supporting (aligned to +/- strand):  ref base C (33/33);  new base T (22/26);  total (55/60)
Fisher's exact test for biased strand distribution p-value = 7.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 115 total aligned reads displayed.

CGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCATTCCTC  >  minE/1169968‑1170094
                                                              |                                                                
cGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATaa                                                                <  1:2645220/65‑1 (MQ=255)
cGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATaa                                                                <  1:3388960/65‑1 (MQ=255)
cGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATaa                                                                <  1:1574095/65‑1 (MQ=255)
cGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATaa                                                                <  1:2587918/65‑1 (MQ=255)
cGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATaa                                                                <  1:3191156/65‑1 (MQ=255)
cGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATaa                                                                <  1:25186/65‑1 (MQ=255)
cGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATaa                                                                <  1:25138/65‑1 (MQ=255)
cGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATaa                                                                <  1:2108220/65‑1 (MQ=255)
cGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATaa                                                                <  1:1036622/65‑1 (MQ=255)
cGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATaa                                                                <  1:2693196/65‑1 (MQ=255)
      aTTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTaa                                                       <  1:1301478/68‑1 (MQ=255)
      aTTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTaa                                                       <  1:3405742/68‑1 (MQ=255)
       ttCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTAt                                                          >  1:565441/1‑64 (MQ=255)
       ttCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAata                                                     <  1:754138/69‑1 (MQ=255)
       ttCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAata                                                     >  1:2943414/1‑69 (MQ=255)
       ttCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAata                                                     <  1:2625686/69‑1 (MQ=255)
       ttCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAata                                                     >  1:173189/1‑69 (MQ=255)
         cTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAatat                                                    >  1:667013/1‑68 (MQ=255)
         cTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAatat                                                    >  1:1539875/1‑68 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:2906247/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:346433/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:2788114/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:254929/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:2367767/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:409438/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:501712/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:2535107/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:1263489/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:1101472/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:1057074/68‑1 (MQ=255)
               ggTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              <  1:953972/68‑1 (MQ=255)
                gTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAatatat                                                  >  1:247689/1‑63 (MQ=255)
                gTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGt                                            >  1:2139581/1‑69 (MQ=255)
                gTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGt                                            >  1:2546430/1‑69 (MQ=255)
                gTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGt                                            >  1:505915/1‑69 (MQ=255)
                     gTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTtat                                       >  1:2013797/1‑69 (MQ=255)
                     gTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTtat                                       >  1:334484/1‑69 (MQ=255)
                     gTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTtat                                       >  1:3367909/1‑69 (MQ=255)
                     gTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTta                                        >  1:2820552/1‑68 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAAt                                                               >  1:3198359/1‑42 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATc                                    >  1:376062/1‑69 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATc                                    >  1:527106/1‑69 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATc                                    >  1:614900/1‑69 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATc                                    >  1:2578679/1‑69 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATc                                    >  1:2183138/1‑69 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATc                                    >  1:124601/1‑69 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATc                                    >  1:1775317/1‑69 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGttt                                          <  1:1392120/63‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:2402365/69‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:926851/69‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:804627/69‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:1117133/69‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:1131542/69‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:1334993/69‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:1733730/69‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:2024867/69‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:2088382/69‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:2663657/69‑1 (MQ=255)
                        gAAAACTGCAAAAGCACATGACATAAACAACATAAGCAAAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:31733/69‑1 (MQ=255)
                               gCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGAt                             <  1:212986/69‑1 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAgg                                              >  1:2723190/1‑49 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATCTATGGATc                            >  1:3373370/1‑67 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATCTATGGATCa                           >  1:3136870/1‑68 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATCTATGGATCa                           >  1:753025/1‑68 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATCTATGGATCa                           >  1:2608635/1‑68 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATCTATGGATCa                           >  1:3137322/1‑68 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATCTATGGATCa                           >  1:1847447/1‑68 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATCTATGGATCa                           >  1:1292735/1‑68 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATCTATGGATCa                           >  1:1018005/1‑68 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATCTATGGATCa                           >  1:2076065/1‑68 (MQ=255)
                                  aaaGCACATGACATAAACAACATAAGCATAATCGTATTAATATATAAGGGTTTTATATCTATGGATCa                           >  1:591860/1‑68 (MQ=255)
                                   aaGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATc                                    <  1:3163003/58‑1 (MQ=255)
                                   aaGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGa                         <  1:1200618/69‑1 (MQ=255)
                                     gCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACa                       <  1:840746/69‑1 (MQ=255)
                                     gCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACa                       <  1:210752/69‑1 (MQ=255)
                                     gCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACa                       <  1:1764596/69‑1 (MQ=255)
                                       acaTGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACata                     >  1:1769862/1‑69 (MQ=255)
                                       acaTGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACata                     >  1:2891178/1‑69 (MQ=255)
                                       acaTGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACat                      >  1:640203/1‑68 (MQ=255)
                                        caTGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACata                     <  1:2185631/68‑1 (MQ=255)
                                          tGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATtc                  <  1:52514/69‑1 (MQ=255)
                                                 aacaacTTAAGCACAATCGTTTTAATATTTAAGGGTTTTATATc                                    <  1:2628911/44‑1 (MQ=255)
                                                 aacaacATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGa            >  1:3143401/1‑68 (MQ=255)
                                                 aacaacATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGa            >  1:255095/1‑68 (MQ=255)
                                                 aacaacATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGa            >  1:639413/1‑68 (MQ=255)
                                                 aacaacATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGa            >  1:5497/1‑68 (MQ=255)
                                                   caacaTAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGt          <  1:2128448/68‑1 (MQ=255)
                                                     acaTAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCAt       <  1:1464665/69‑1 (MQ=255)
                                                     acaTAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCAt       <  1:240120/69‑1 (MQ=255)
                                                     acaTAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCAt       <  1:1018522/69‑1 (MQ=255)
                                                     acaTAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCAt       <  1:1264225/69‑1 (MQ=255)
                                                     acaTAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCAt       <  1:382542/69‑1 (MQ=255)
                                                      caTAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCAtt      >  1:174811/1‑69 (MQ=255)
                                                      caTAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCAtt      >  1:2868286/1‑69 (MQ=255)
                                                      caTAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCAtt      >  1:2429713/1‑69 (MQ=255)
                                                      caTAAGCACAATCGAATTAATATATAAGGGTTTTATATCTATGTATCAGACATATTCTCTGGAGTCAt       <  1:1327856/68‑1 (MQ=255)
                                                          aGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCATTCCTc  >  1:2148839/1‑69 (MQ=255)
                                                          aGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCATTCCTc  >  1:1456961/1‑69 (MQ=255)
                                                          aGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCATTCCTc  >  1:2931397/1‑69 (MQ=255)
                                                          aGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCATTCCTc  >  1:2704181/1‑69 (MQ=255)
                                                              |                                                                
CGTCACATTCTTGATGGTATAGTCGAAAACTGCAAAAGCACATGACATAAACAACATAAGCACAATCGTATTAATATATAAGGGTTTTATATCTATGGATCAGACATATTCTCTGGAGTCATTCCTC  >  minE/1169968‑1170094

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