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 2,080,902 A→G 40.5% V199V (GTA→GTG)  exuT → hexuronate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,080,9020AG40.5% 29.3 / 55.6 79V199V (GTA→GTG) exuThexuronate transporter
Reads supporting (aligned to +/- strand):  ref base A (42/5);  new base G (22/10);  total (64/15)
Fisher's exact test for biased strand distribution p-value = 3.85e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

TACTTTAACGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGATGGCATG  >  minE/2080837‑2080967
                                                                 |                                                                 
tACTTTAACGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:1010072/1‑69 (MQ=255)
       aCGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTGATGCACAGc                                                          <  1:2444220/68‑1 (MQ=255)
       aCGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTGATGCACAGc                                                          <  1:2723569/68‑1 (MQ=255)
       aCGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTGATGCACAGc                                                          <  1:1001239/68‑1 (MQ=255)
       aCGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTGATGCACAGc                                                          <  1:223454/68‑1 (MQ=255)
       aCGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTGATGCACAGc                                                          <  1:220075/68‑1 (MQ=255)
       aCGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTGATGCACAGc                                                          <  1:157647/68‑1 (MQ=255)
       aCGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTGATGCACAGc                                                          <  1:1501591/68‑1 (MQ=255)
       aCGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTGATGCACAGc                                                          <  1:1246655/68‑1 (MQ=255)
       aCGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTGATGCACAGc                                                          <  1:1147021/68‑1 (MQ=255)
       aCGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTGATGCACAGc                                                          <  1:1230511/68‑1 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:951963/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:2357515/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:110615/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:1069969/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:3077518/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:3128544/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:2805049/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:320928/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:3232894/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:3396990/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:277665/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:1511902/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:810750/1‑59 (MQ=255)
          tAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATg                                                                >  1:662451/1‑59 (MQ=255)
          aaGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAAt                                                                 >  1:1773526/2‑58 (MQ=255)
           aGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATGCACAGCTGGCa                                                     <  1:2634010/69‑1 (MQ=255)
                       tGGTGCAATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTat                                         <  1:1271300/69‑1 (MQ=255)
                        ggTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTatc                                        <  1:3132080/69‑1 (MQ=255)
                        ggTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTatc                                        <  1:571279/69‑1 (MQ=255)
                        ggTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAAACGTAATGCACAGCTGGCAGATGGCATTTatc                                        <  1:1191662/69‑1 (MQ=255)
                              atgatTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTcc                                  >  1:2881057/1‑69 (MQ=255)
                              atgatTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTcc                                  >  1:1282779/1‑69 (MQ=255)
                                            gcTGGTGGTATGGTAAATCGTGATGCACAGCTGGCAGATGGCATTTatca                                       >  1:1527472/1‑50 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:1051113/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:2792876/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:282854/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:2742136/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:2837666/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:2846525/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:3176098/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:3207102/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:328353/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:348555/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:5266/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:680434/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:166267/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:1268970/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:1449880/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:1210730/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:1518754/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:1546807/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:162148/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:1995766/1‑69 (MQ=255)
                                            gcTGGTGGTATGGGCAATCGTGATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCGTTGAGCtt                    >  1:2520287/1‑69 (MQ=255)
                                               ggtggtATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTAt                 >  1:2484880/1‑69 (MQ=255)
                                               ggtggtATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTAt                 >  1:508276/1‑69 (MQ=255)
                                               ggtggtATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTAt                 >  1:1624467/1‑69 (MQ=255)
                                               ggtggtATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTAt                 >  1:2870623/1‑69 (MQ=255)
                                               ggtggtATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTAt                 >  1:1441466/1‑69 (MQ=255)
                                               ggtggtATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTAt                 >  1:1708862/1‑69 (MQ=255)
                                               ggtggtATGCGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTAt                 >  1:645586/1‑69 (MQ=255)
                                                        ggCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAg                       >  1:733316/1‑54 (MQ=255)
                                                        ggCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTAt                 >  1:329110/1‑60 (MQ=255)
                                                        ggCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGat        >  1:2029536/1‑69 (MQ=255)
                                                        ggCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGat        >  1:2143152/1‑69 (MQ=255)
                                                        ggCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGat        >  1:2306010/1‑69 (MQ=255)
                                                        ggCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGat        >  1:1287096/1‑69 (MQ=255)
                                                        ggCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGat        >  1:2664561/1‑69 (MQ=255)
                                                              cGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGatggcatg  >  1:797075/1‑69 (MQ=255)
                                                              cGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGatggcatg  >  1:646260/1‑69 (MQ=255)
                                                              cGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGatggcatg  >  1:2189441/1‑69 (MQ=255)
                                                              cGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGatggcatg  >  1:236367/1‑69 (MQ=255)
                                                              cGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGatggcatg  >  1:2729861/1‑69 (MQ=255)
                                                              cGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGatggcatg  >  1:1879581/1‑69 (MQ=255)
                                                              cGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGatggcatg  >  1:3164235/1‑69 (MQ=255)
                                                              cGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGatggcat   >  1:3363947/1‑68 (MQ=255)
                                                              cGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGatggcat   >  1:2048337/1‑68 (MQ=255)
                                                              cGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGatggca    >  1:2044476/1‑67 (MQ=255)
                                                                 |                                                                 
TACTTTAACGTAGGTTCTTCGATTGGTGCGATGATTGCGCCGCCGCTGGTGGTATGGGCAATCGTAATGCACAGCTGGCAGATGGCATTTATCATCTCCGGTGCATTGAGCTTTATCTGGGCGATGGCATG  >  minE/2080837‑2080967

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