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 2,895,566 T→C 28.2% N200N (AAT→AAC)  yjfF → predicted sugar transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,895,5660TC28.2% 58.6 / 23.7 60N200N (AAT→AAC) yjfFpredicted sugar transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (29/14);  new base C (6/11);  total (35/25)
Fisher's exact test for biased strand distribution p-value = 4.04e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCTCTCCACCG  >  minE/2895498‑2895621
                                                                    |                                                       
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:1085159/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:2261656/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:2083928/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:595759/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:1957895/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:617800/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:3427100/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:685305/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:2472145/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:2724916/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:1576759/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:836640/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:2897632/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:1326685/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:296348/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:973653/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:1001808/1‑69 (MQ=255)
ttCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:3127747/1‑69 (MQ=255)
tcccTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAAt                                                         >  1:24743/3‑69 (MQ=255)
  ccTCGCGCATCGTACCCGTTTTGGTAATGAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCt                                                       <  1:1597481/69‑1 (MQ=255)
  ccTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCt                                                       <  1:2768870/69‑1 (MQ=255)
  ccTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCt                                                       <  1:2746431/69‑1 (MQ=255)
  ccTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCt                                                       <  1:24953/69‑1 (MQ=255)
  ccTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCt                                                       <  1:3219166/69‑1 (MQ=255)
  ccTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCt                                                       <  1:360277/69‑1 (MQ=255)
  ccTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCt                                                       <  1:3201025/69‑1 (MQ=255)
  ccTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCt                                                       <  1:1613675/69‑1 (MQ=255)
   cTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCt                                                       <  1:1254983/68‑1 (MQ=255)
                 ccGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCt                                                       <  1:3234169/54‑1 (MQ=255)
                              cAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCgcagc                                 >  1:479066/1‑63 (MQ=255)
                              cAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCgcagc                                 >  1:3211994/1‑63 (MQ=255)
                              cAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCgcagc                                 >  1:835088/1‑63 (MQ=255)
                              cAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCgcagc                                 >  1:1608217/1‑63 (MQ=255)
                              cAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCgcagc                                 >  1:2703342/1‑63 (MQ=255)
                              cAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCgcagc                                 >  1:252720/1‑63 (MQ=255)
                              cAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCgcagc                                 >  1:252082/1‑63 (MQ=255)
                               aGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACt                           >  1:3105076/1‑68 (MQ=255)
                               aGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTa                          >  1:3287985/1‑69 (MQ=255)
                               aGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTa                          >  1:2471522/1‑69 (MQ=255)
                               aGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTa                          >  1:2410567/1‑69 (MQ=255)
                               aGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGAAGGGGATTTCCACTCGCAGCACCACTa                          >  1:1632983/1‑69 (MQ=255)
                                      cGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCa                    >  1:179854/1‑68 (MQ=255)
                                      cGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCa                    >  1:3340025/1‑68 (MQ=255)
                                      cGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCa                    >  1:1909067/1‑68 (MQ=255)
                                      cGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCa                    >  1:2099075/1‑68 (MQ=255)
                                      cGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCa                    >  1:428860/1‑68 (MQ=255)
                                      cGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCa                    >  1:1111166/1‑68 (MQ=255)
                                        ccATTGGCGGCAACGCAACGTCGGCAAACCTGATGGGGATTTTCACTTGCAGCACCACTATTCGCAtt                  <  1:842929/68‑1 (MQ=255)
                                        ccATTGGCGGCAACGCAACGTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCAtt                  <  1:752191/68‑1 (MQ=255)
                                        ccATTGGCGGCAACGCAACGTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCAtt                  <  1:912303/68‑1 (MQ=255)
                                        ccATTGGCGGCAACGCAACGTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCAtt                  <  1:987600/68‑1 (MQ=255)
                                        ccATTGGCGGCAACGCAACGTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCAtt                  <  1:1240496/68‑1 (MQ=255)
                                        ccATTGGCGGCAACGCAACGTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCAtt                  <  1:2474923/68‑1 (MQ=255)
                                        ccATTGGCGGCAACGCAACGTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCAtt                  <  1:1484414/68‑1 (MQ=255)
                                        ccATTGGCGGCAACGCAACGTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCAtt                  <  1:1578840/68‑1 (MQ=255)
                                        ccATTGGCGGCAACGCAACGTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCAtt                  <  1:1943777/68‑1 (MQ=255)
                                        ccATTGGCAGCAACGCAACGTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCAtt                  <  1:2119448/68‑1 (MQ=255)
                                         cATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCTCATTta                <  1:443221/69‑1 (MQ=255)
                                         cATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTta                <  1:2115736/69‑1 (MQ=255)
                                             ggcggcAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTatat             >  1:1901157/1‑68 (MQ=255)
                                             ggcggcAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTatat             >  1:630503/1‑68 (MQ=255)
                                             ggcggcAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATg            >  1:819728/1‑69 (MQ=255)
                                                  caacgcaacgTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCtctc       <  1:348295/69‑1 (MQ=255)
                                                  caacgcaacgTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCtctc       <  1:1833623/69‑1 (MQ=255)
                                                  caacgcaacgTCGGCAACCCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCATTTATATGc           >  1:2966348/1‑65 (MQ=255)
                                                  caacgcaacgTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCATTTatat             >  1:1127501/1‑63 (MQ=255)
                                                  caacgcaacgTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCATTTATATg            >  1:1320934/1‑64 (MQ=255)
                                                  caacgcaacgTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCATTTATATGc           >  1:489141/1‑65 (MQ=255)
                                                  caacgcaacgTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCATTTATATGc           >  1:2447364/1‑65 (MQ=255)
                                                  caacgcaacgTCGGCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCATTTATATGc           >  1:2582180/1‑65 (MQ=255)
                                                   aacgcaacgTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCTCTcc      >  1:2297135/1‑69 (MQ=255)
                                                   aacgcaacgTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCTCTcc      >  1:136321/1‑69 (MQ=255)
                                                   aacgcaacgTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCTCTcc      >  1:863444/1‑69 (MQ=255)
                                                      gcaacgTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCTCTCCAc    >  1:609906/1‑68 (MQ=255)
                                                      gcaacgTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCTCTCCAc    >  1:2082115/1‑68 (MQ=255)
                                                      gcaacgTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCTCTCCAc    >  1:503696/1‑68 (MQ=255)
                                                      gcaacgTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCTCTCCAc    >  1:344619/1‑68 (MQ=255)
                                                       caacgTCGGCCAATCTGATGGCGATTTCCACTCGCAGCACCACAATTCGCATTTATATGCTCTCCACCg  >  1:2284135/1‑69 (MQ=255)
                                                              ggCAAACCTGATGGGGATTTCCACTTGCAGCACCACTATTCGCAtt                  <  1:2984543/46‑1 (MQ=255)
                                                                    |                                                       
TTCCTCGCGCATCGTACCCGTTTTGGTAATCAGGTATACGCCATTGGCGGCAACGCAACGTCGGCGAATCTGATGGGGATTTCCACTCGCAGCACCACTATTCGCATTTATATGCTCTCCACCG  >  minE/2895498‑2895621

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