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 1,071,831 A→G 54.3% A228A (GCA→GCG)  mdtK → multidrug efflux system transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,071,8310AG54.3% 12.0 / 55.2 70A228A (GCA→GCG) mdtKmultidrug efflux system transporter
Reads supporting (aligned to +/- strand):  ref base A (19/13);  new base G (18/20);  total (37/33)
Fisher's exact test for biased strand distribution p-value = 3.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGATTGCGCTGGCACTGTT  >  minE/1071770‑1071896
                                                             |                                                                 
tGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCg                                                            >  1:1312472/1‑69 (MQ=255)
  ttttCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt                                                          <  1:2634566/68‑1 (MQ=255)
  gTTTCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAATCCCGAt                                                          <  1:438685/69‑1 (MQ=255)
  gTTTCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt                                                          <  1:1103953/69‑1 (MQ=255)
  gTTTCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt                                                          <  1:2494882/69‑1 (MQ=255)
  gTTTCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt                                                          <  1:900123/69‑1 (MQ=255)
  gTTTCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt                                                          <  1:169490/69‑1 (MQ=255)
   tttCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt                                                          <  1:492933/68‑1 (MQ=255)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:1107394/59‑1 (MQ=38)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:2606583/59‑1 (MQ=38)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:1780806/59‑1 (MQ=38)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:3246860/59‑1 (MQ=38)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:1634031/59‑1 (MQ=38)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:3372982/59‑1 (MQ=38)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:1609348/59‑1 (MQ=38)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:371985/59‑1 (MQ=38)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:1331224/59‑1 (MQ=38)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:927878/59‑1 (MQ=38)
          cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:1178269/59‑1 (MQ=38)
           aTTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg                                                            <  1:2239959/58‑1 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:3043954/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:2155317/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:2064647/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:1149615/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:1172495/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:2733879/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:2869420/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:1850529/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:1470554/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:898264/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:306600/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:1644834/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:641629/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:350549/1‑51 (MQ=38)
             tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag                                                                >  1:394073/1‑51 (MQ=38)
                aCGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGa                                             <  1:563197/68‑1 (MQ=255)
                     cccGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGa                                        >  1:667816/1‑68 (MQ=255)
                     cccGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGa                                        >  1:630092/1‑68 (MQ=255)
                                ctcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:2380259/3‑69 (MQ=255)
                                cgcgATATTCTTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:3115838/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAAGCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:2586653/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:1252358/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:1612842/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:1528506/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:1469711/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:2885572/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:1896273/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:2762116/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:1954121/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:1116663/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:94848/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:2530081/1‑69 (MQ=255)
                                cgcgATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTc                            >  1:2341858/1‑69 (MQ=255)
                                    atatTCGTAACGAAAAAGGCACCGCGAAGCCCGAt                                                          <  1:1702107/35‑1 (MQ=37)
                                         cGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGcc                    <  1:2708297/68‑1 (MQ=255)
                                         cGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGcc                    <  1:2319171/68‑1 (MQ=255)
                                         cGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGcc                    <  1:340227/68‑1 (MQ=255)
                                         cGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGcc                    <  1:2324192/68‑1 (MQ=255)
                                         cGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGcc                    <  1:2153868/68‑1 (MQ=255)
                                         cGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGcc                    <  1:2014558/68‑1 (MQ=255)
                                          gTAACGAAAAAGGCGCCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:1657461/1‑69 (MQ=255)
                                          gTAACGAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGCAACGACTGATTCAACTCGGTTTGCCGa                  >  1:2916603/1‑69 (MQ=255)
                                          gTAACGAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:1300531/1‑69 (MQ=255)
                                          gTAACGAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:2065913/1‑69 (MQ=255)
                                          gTAACGAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:1269930/1‑69 (MQ=255)
                                          gTAACGAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:1589939/1‑69 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTg                                     >  1:1620723/1‑45 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGa                                    >  1:3079211/1‑46 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:147530/1‑64 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:2534560/1‑64 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:1410422/1‑64 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:592909/1‑64 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:2943161/1‑64 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:2838307/1‑64 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:2784097/1‑64 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:1637987/1‑64 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:934729/1‑64 (MQ=255)
                                               gAAAAAGGCACCGCGAAGCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGa                  >  1:1111982/1‑64 (MQ=255)
                                                       cACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGATTGCGCTGGCACt     >  1:84985/1‑69 (MQ=255)
                                                          cgtaaaaCCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGATTGCGCTGGCACTGtt  <  1:1223078/66‑1 (MQ=255)
                                                          cGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGATTGCGCTGGCACTGtt  <  1:798052/69‑1 (MQ=255)
                                                          cGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGATTGCGCTGGCACTGtt  <  1:978888/69‑1 (MQ=255)
                                                          cGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGATTGCGCTGGCACTGtt  <  1:2009384/69‑1 (MQ=255)
                                                          cGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGATTGCGCTGGCACTGtt  <  1:887007/69‑1 (MQ=255)
                                                          cGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGATTGCGCTGGCACTGtt  <  1:3003828/69‑1 (MQ=255)
                                                          cGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGATTGCGCTGGCACTGtt  <  1:2235072/69‑1 (MQ=255)
                                                             |                                                                 
TGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGACTGATTCAACTCGGTTTGCCGATTGCGCTGGCACTGTT  >  minE/1071770‑1071896

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