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 374,062 T→A 22.3% L304L (CTT→CTA)  fepE → regulator of length of O‑antigen component of lipopolysaccharide chains

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE374,0620TA22.3% 128.6 / 32.9 76L304L (CTT→CTA) fepEregulator of length of O‑antigen component of lipopolysaccharide chains
Reads supporting (aligned to +/- strand):  ref base T (24/35);  new base A (15/2);  total (39/37)
Fisher's exact test for biased strand distribution p-value = 6.71e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.36e-01

TGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAGCC  >  minE/373995‑374129
                                                                   |                                                                   
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTATGTAATCGGCAGTATCTTg                                                                    <  1:1221410/69‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTg                                                                    <  1:1541267/69‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTg                                                                    <  1:322627/69‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTg                                                                    <  1:2254241/69‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTg                                                                    <  1:2816177/69‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTg                                                                    <  1:1463102/69‑1 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:1639395/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:1081348/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:164307/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:2046198/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:2164767/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:2566120/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:281772/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:3068431/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:3330600/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:570703/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:69747/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:999151/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt                                                          >  1:1469637/1‑68 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAt                                                           >  1:2823020/1‑67 (MQ=255)
           aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAt                                                           >  1:3224672/1‑67 (MQ=255)
                    aCTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGca                                                <  1:1633945/69‑1 (MQ=255)
                    aCTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGca                                                <  1:2906146/69‑1 (MQ=255)
                    aCTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGca                                                <  1:3069638/69‑1 (MQ=255)
                    aCTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGca                                                <  1:421085/69‑1 (MQ=255)
                     cTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGca                                                <  1:877622/68‑1 (MQ=255)
                     cTGACGTTGCGGAACTGAACGGCGAATTACGTAATCGGCATTATCTTGTCGAGCAATTAACAAAAGca                                                <  1:3330849/68‑1 (MQ=255)
                      tGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCATTATCTTGTCGAGCAATTAACAAAAGca                                                <  1:2455814/67‑1 (MQ=255)
                             gCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAAtt                                                          <  1:2196004/50‑1 (MQ=255)
                                 aattGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAATTAACAAAAACAAATATCAACGAtg                                   <  1:1984409/66‑1 (MQ=255)
                                 aattGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAATTAACAAAAACAAATATCAACGAtg                                   <  1:293724/66‑1 (MQ=255)
                                     gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:42469/1‑69 (MQ=255)
                                     gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:828126/1‑69 (MQ=255)
                                     gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:1630811/1‑69 (MQ=255)
                                     gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:2241079/1‑69 (MQ=255)
                                     gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:1681594/1‑69 (MQ=255)
                                     gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATCTCAACGATGTGa                                >  1:991840/1‑68 (MQ=255)
                                        cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:2290931/69‑1 (MQ=255)
                                        cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:2344100/69‑1 (MQ=255)
                                        cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:2945646/69‑1 (MQ=255)
                                        cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:1511416/69‑1 (MQ=255)
                                        cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:783135/69‑1 (MQ=255)
                                        cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:1984204/69‑1 (MQ=255)
                                         ggTGAATTACGTAATCGTCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:571464/68‑1 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            >  1:599236/1‑66 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:3047758/66‑1 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:305411/66‑1 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            >  1:1159874/1‑66 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            >  1:1528649/1‑66 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:342871/66‑1 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            >  1:1812824/1‑66 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:1686795/66‑1 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            >  1:1172768/1‑66 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:1497983/66‑1 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            >  1:2230816/1‑66 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            >  1:2889572/1‑66 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:2581275/66‑1 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:1259591/66‑1 (MQ=255)
                                           tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            >  1:1299900/1‑66 (MQ=255)
                                            gAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt                            <  1:3189397/65‑1 (MQ=255)
                                                     aaTCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTaaa               <  1:2373372/69‑1 (MQ=255)
                                                         ggCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATc           >  1:2536246/1‑69 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGttt      <  1:2540404/67‑2 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTa      <  1:2941293/67‑1 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTa      <  1:1674211/67‑1 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTa      <  1:1834331/67‑1 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTa      <  1:1258303/67‑1 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAg    >  1:12458/1‑69 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAg    >  1:3323907/1‑69 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAg    >  1:3076477/1‑69 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAg    >  1:2123520/1‑69 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAg    >  1:3428663/1‑69 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAg    >  1:2075059/1‑69 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAg    >  1:2445386/1‑69 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAg    >  1:2411656/1‑69 (MQ=255)
                                                                tCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAg    >  1:2759691/1‑69 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:1047138/1‑40 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:637199/1‑40 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:1235432/1‑40 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:3263899/1‑40 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:186166/1‑40 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:2893124/1‑40 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:2120617/1‑40 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:2616303/1‑40 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa                               >  1:2473038/1‑40 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGa                                >  1:427608/1‑39 (MQ=255)
                                                                  ttGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAGcc  >  1:3055954/1‑69 (MQ=255)
                                                                   |                                                                   
TGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATCAGTTAAGCC  >  minE/373995‑374129

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