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 1,207,129 G→C 39.5% G44G (GGG→GGC)  manY → mannose‑specific enzyme IIC component of PTS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,207,1290GC39.5% 51.2 / 75.3 81G44G (GGG→GGC) manYmannose‑specific enzyme IIC component of PTS
Reads supporting (aligned to +/- strand):  ref base G (16/33);  new base C (15/17);  total (31/50)
Fisher's exact test for biased strand distribution p-value = 2.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATCCTCGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAACATCGG  >  minE/1207063‑1207197
                                                                  |                                                                    
aaTCCTCGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGa                                                                    <  1:1217155/69‑1 (MQ=255)
aaTCCTCGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGa                                                                    <  1:3367515/69‑1 (MQ=255)
    cTCGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGatat                                                                 >  1:915093/1‑68 (MQ=255)
    cTCGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGatat                                                                 >  1:2006749/1‑68 (MQ=255)
    cTCGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGatat                                                                 >  1:2111676/1‑68 (MQ=255)
    cTCGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGatat                                                                 >  1:3391112/1‑68 (MQ=255)
      cGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGATATGaa                                                              <  1:1659146/69‑1 (MQ=255)
      cGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGATATGaa                                                              <  1:3186630/69‑1 (MQ=255)
      cGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGATATGaa                                                              <  1:293368/69‑1 (MQ=255)
      cGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGATATGaa                                                              <  1:2340736/69‑1 (MQ=255)
       gATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGATATGaa                                                              <  1:1186000/68‑1 (MQ=255)
               tCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGtat                                                     <  1:167776/69‑1 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:2849273/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:1814994/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:2181206/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:2422254/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:2448806/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:3353032/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:2690204/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:1018558/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:3323541/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:3117648/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:3121458/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:332352/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:3236742/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:1578252/1‑51 (MQ=255)
                    ttCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGCGata                                                                  >  1:1489937/1‑51 (MQ=255)
                     tCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGtattattat                                               >  1:2826822/1‑69 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTTTTATTATCGGTGGTACGCTgg                                 <  1:2940676/68‑1 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTgg                                 <  1:16029/68‑1 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTgg                                 <  1:504809/68‑1 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTgg                                 <  1:1201605/68‑1 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTgg                                 <  1:2946310/68‑1 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTgg                                 <  1:2698073/68‑1 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTgg                                 <  1:1302291/68‑1 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTgg                                 <  1:1398153/68‑1 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTgg                                 <  1:1459238/68‑1 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTgg                                 <  1:2308911/68‑1 (MQ=255)
                                    cgcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGa                                <  1:1229070/69‑1 (MQ=255)
                                     gcgTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTgg                                 <  1:2129547/67‑1 (MQ=255)
                                            cccTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATg                            >  1:1766744/1‑65 (MQ=255)
                                              cTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATcgc                       <  1:1495791/68‑1 (MQ=255)
                                              cTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATcgc                       <  1:1395819/68‑1 (MQ=255)
                                              cTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATcgc                       <  1:303324/68‑1 (MQ=255)
                                              cTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATcgc                       <  1:1625534/68‑1 (MQ=255)
                                              cTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATcgc                       <  1:1465974/68‑1 (MQ=255)
                                               tggtggGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATcgc                       <  1:1814743/67‑1 (MQ=255)
                                                      tATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctg              <  1:1204067/69‑1 (MQ=255)
                                                      tATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctg              >  1:2994188/1‑69 (MQ=255)
                                                      tATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctg              <  1:715635/69‑1 (MQ=255)
                                                      tATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctg              <  1:3343699/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:1584468/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:2129680/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:3185455/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:15312/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:1245991/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:2801708/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:1518240/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:126497/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:1839084/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:2550017/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:1320324/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:2348212/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:2347612/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:2076075/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:2110741/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:2231826/69‑1 (MQ=255)
                                                       aTCGTTCTTGGCGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             <  1:2180000/69‑1 (MQ=255)
                                                        tCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATcgcg                      >  1:1144933/1‑59 (MQ=255)
                                                        tCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCgctgggctgg             >  1:932019/1‑68 (MQ=255)
                                                        tCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGAgctgggctgg             >  1:1187170/1‑68 (MQ=255)
                                                         cGTTCTTGGGGATATGAAAACCGGTTTTATTATCGGTGGTACGCTGGATATGATCGCgctgggctg              <  1:662378/66‑1 (MQ=255)
                                                          gTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATg          >  1:2756693/1‑69 (MQ=255)
                                                          gTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATg          >  1:1178014/1‑69 (MQ=255)
                                                           ttCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATg          <  1:3013980/68‑1 (MQ=255)
                                                           ttCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATg          <  1:2420457/68‑1 (MQ=255)
                                                             cTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAAc       >  1:2572702/1‑69 (MQ=255)
                                                             cTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAAc       >  1:3361052/1‑69 (MQ=255)
                                                             cTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAAc       >  1:1231143/1‑69 (MQ=255)
                                                             cTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAAc       <  1:3426428/69‑1 (MQ=255)
                                                             cTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAAc       >  1:692725/1‑69 (MQ=255)
                                                                  ggATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAACATc    <  1:68166/67‑1 (MQ=255)
                                                                  ggATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAACATc    <  1:1120171/67‑1 (MQ=255)
                                                                  ggATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAACATc    <  1:1039640/67‑1 (MQ=255)
                                                                  ggATATGAAAACCGGTATTA‑TATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAACATCgg  <  1:3231610/68‑1 (MQ=255)
                                                                  ggATATGAAAACCGGTATTA‑TATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAACATCgg  <  1:3227653/68‑1 (MQ=255)
                                                                  |                                                                    
AATCCTCGATGAATTTCAGTTTCACCGTCCGCTAATCGCGTGTACCCTGGTGGGTATCGTTCTTGGGGATATGAAAACCGGTATTATTATCGGTGGTACGCTGGAAATGATCGCGCTGGGCTGGATGAACATCGG  >  minE/1207063‑1207197

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