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	1,794,406	T→C	44.6%	R424R (CGT→CGC)	gabP →	gamma‑aminobutyrate transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,794,406	0	T	C	44.6%	10.6 / 59.3	74	R424R (CGT→CGC)	gabP	gamma‑aminobutyrate transporter
Reads supporting (aligned to +/- strand): ref base T (16/25); new base C (22/11); total (38/36)
Fisher's exact test for biased strand distribution p-value = 2.13e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.48e-01

TATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTGCCAAT  >  minE/1794341‑1794474

tATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATtccgtccg                                                                   >  1:2517857/1‑69 (MQ=255)

        gCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCTCAACa                                                           <  1:182493/69‑1 (MQ=255)

        gCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACa                                                           <  1:2214263/69‑1 (MQ=255)

        gCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACa                                                           <  1:2973144/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:2164703/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:448692/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:1880599/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:2362309/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:2390887/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:400466/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:687255/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:676771/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:145835/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:2956127/69‑1 (MQ=255)

          tCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:1185814/69‑1 (MQ=255)

           cACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACa                                                           >  1:1342394/1‑66 (MQ=255)

           cACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt                                                         <  1:2366294/68‑1 (MQ=255)

              cTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGa                                                     >  1:2683049/1‑69 (MQ=255)

              cTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGa                                                     >  1:2876628/1‑69 (MQ=255)

              cTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGa                                                     >  1:2977057/1‑69 (MQ=255)

              cTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGa                                                     >  1:567682/1‑69 (MQ=255)

                   tAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTg                                                 <  1:2279598/68‑1 (MQ=255)

                   tAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTg                                                 <  1:863529/68‑1 (MQ=255)

                   tAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTg                                                 <  1:404045/68‑1 (MQ=255)

                   tAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTg                                                 <  1:1566156/68‑1 (MQ=255)

                   tAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTg                                                 <  1:1227592/68‑1 (MQ=255)

                        aTCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTcc                                           <  1:357191/69‑1 (MQ=255)

                        aTCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTcc                                           <  1:464392/69‑1 (MQ=255)

                        aTCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTcc                                           >  1:98894/1‑69 (MQ=255)

                        aTCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTcc                                           <  1:3141101/69‑1 (MQ=255)

                        aTCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTcc                                           <  1:2386640/69‑1 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:37858/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:2654851/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:2682354/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:2743072/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:622630/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:1118557/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:3001078/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:3196290/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:3280584/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:3281281/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:3283124/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:335394/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:60755/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:2060746/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:2568745/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:2547732/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:1617109/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:2312535/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:161866/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:937902/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGCCCgg                                                                  >  1:1817077/1‑44 (MQ=255)

                          cGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTACGCCCgg                                                                  >  1:5519/1‑44 (MQ=255)

                            gCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACa                                                           <  1:2213713/49‑1 (MQ=255)

                              tttATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCgg                                      >  1:48729/1‑68 (MQ=255)

                              tttATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCgg                                      >  1:927766/1‑68 (MQ=255)

                              tttATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCgg                                      >  1:1150287/1‑68 (MQ=255)

                              tttATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCgg                                      >  1:2502233/1‑68 (MQ=255)

                              tttATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCgg                                      >  1:2127256/1‑68 (MQ=255)

                                     ccTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCGGCttatta                               >  1:3095821/1‑68 (MQ=255)

                                     ccTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCGGCttatta                               >  1:1384324/1‑68 (MQ=255)

                                     ccTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCGGCttatta                               >  1:2127877/1‑68 (MQ=255)

                                                  aGTGATGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:1022080/47‑1 (MQ=255)

                                                  aGTGATGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:570059/47‑1 (MQ=255)

                                                  aGTGATGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:3417774/47‑1 (MQ=255)

                                                  aGTGATGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:627197/47‑1 (MQ=255)

                                                  aGTGATGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:232601/47‑1 (MQ=255)

                                                  aGTGATGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:2031408/47‑1 (MQ=255)

                                                  aGTGATGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:1939981/47‑1 (MQ=255)

                                                  aGTGATGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:1509210/47‑1 (MQ=255)

                                                  aGTGATGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:1384962/47‑1 (MQ=255)

                                                  aGTGAAGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:792008/47‑1 (MQ=255)

                                                   gTGATGCTATTCCGCCCGGCGCAACAGTTAGAAGTGATCTCCACCg                                       <  1:1886259/46‑1 (MQ=255)

                                                      aTGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGt             >  1:108931/1‑69 (MQ=255)

                                                      aTGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCT‑CACCGGCTTATTAGCGATAGGGATTATCTGTa            >  1:3412744/1‑69 (MQ=255)

                                                             tccgtccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTg       >  1:2647694/1‑68 (MQ=255)

                                                             tccgtccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTg       >  1:2471945/1‑68 (MQ=255)

                                                              ccgtccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTAc           >  1:2521479/1‑63 (MQ=255)

                                                              ccgtccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTGcc     >  1:2662503/1‑69 (MQ=255)

                                                              ccgtccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTGcc     >  1:183791/1‑69 (MQ=255)

                                                              ccgtccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTGcc     >  1:1563935/1‑69 (MQ=255)

                                                              ccgtccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTGc      >  1:1620764/1‑68 (MQ=255)

                                                                 tccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAgg                       <  1:2226965/48‑1 (MQ=255)

                                                                 tccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTGGCAAt  <  1:2903712/69‑1 (MQ=255)

                                                                 tccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTGCCAAt  <  1:420738/69‑1 (MQ=255)

                                                                 tccgGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTGCCAAt  <  1:958695/69‑1 (MQ=255)

TATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAGAAGTGATCTCCACCGGCTTATTAGCGATAGGGATTATCTGTACCGTGCCAAT  >  minE/1794341‑1794474

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