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	1,970,324	C→A	40.3%	A156A (GCG→GCT)	speB ←	agmatinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,970,324	0	C	A	40.3%	41.1 / 57.2	67	A156A (GCG→GCT)	speB	agmatinase
Reads supporting (aligned to +/- strand): ref base C (27/13); new base A (8/19); total (35/32)
Fisher's exact test for biased strand distribution p-value = 3.01e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.04e-01

GATCAGACCTTCTTTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAG  >  minE/1970264‑1970388

gATCAGACCTTCTTTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGt                                                          <  1:1000225/69‑1 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:1931790/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:2055315/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:1620429/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:1603260/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:2070709/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:138123/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:1311623/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:2555792/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:2617744/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:2707844/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:1144428/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:3233973/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTggg                                               >  1:561782/1‑69 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTgg                                                >  1:2884128/1‑68 (MQ=255)

           cttTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTgg                                                >  1:1935820/1‑68 (MQ=255)

                    cgGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAg                                       <  1:629802/68‑1 (MQ=255)

                     ggTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAgtg                                     <  1:2318086/69‑1 (MQ=255)

                     ggTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAgtg                                     <  1:566731/69‑1 (MQ=255)

                       tataGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAgtg                                     <  1:1617560/67‑1 (MQ=255)

                         taGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAgtgt                                    >  1:1459129/1‑66 (MQ=255)

                         taGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTAcc                                 >  1:1085132/1‑69 (MQ=255)

                           gAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAg                               >  1:245730/1‑69 (MQ=255)

                           gAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAg                               >  1:961685/1‑69 (MQ=255)

                           gAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAg                               >  1:124877/1‑69 (MQ=255)

                                 aGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCAt                         <  1:552676/69‑1 (MQ=255)

                                 aGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCAt                         <  1:2451185/69‑1 (MQ=255)

                                 aGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCAt                         <  1:1142694/69‑1 (MQ=255)

                                    gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTggg                                               >  1:2499323/1‑44 (MQ=255)

                                    gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt                      >  1:1753014/1‑69 (MQ=255)

                                    gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt                      >  1:2928915/1‑69 (MQ=255)

                                    gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt                      >  1:305247/1‑69 (MQ=255)

                                    gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt                      >  1:1112333/1‑69 (MQ=255)

                                    gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt                      >  1:817956/1‑69 (MQ=255)

                                    gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt                      >  1:1289773/1‑69 (MQ=255)

                                    gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt                      >  1:2514388/1‑69 (MQ=255)

                                     ccGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTg                     >  1:407117/1‑69 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:32810/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:830361/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:3153102/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:2709940/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:40637/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:1058394/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:1052721/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:7738/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:11975/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:843088/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:236146/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:936784/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:2256012/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:941592/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:1583200/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:1849621/69‑1 (MQ=255)

                                        tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATATTGCCg                  <  1:441462/69‑1 (MQ=255)

                                        tGGGCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:2211694/69‑1 (MQ=255)

                                         ggTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg                  <  1:1698364/68‑1 (MQ=255)

                                                ttCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCtt          >  1:2755800/1‑69 (MQ=255)

                                                ttCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCtt          >  1:1837137/1‑69 (MQ=255)

                                                  cacaACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTc         >  1:1231747/1‑68 (MQ=255)

                                                  cacaACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCg        >  1:1004493/1‑69 (MQ=255)

                                                  cacaACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCg        >  1:1956779/1‑69 (MQ=255)

                                                  cacaACAGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCg        >  1:438920/1‑69 (MQ=255)

                                                    caACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGc       <  1:2892205/68‑1 (MQ=255)

                                                    caACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGc       <  1:1270855/68‑1 (MQ=255)

                                                    caACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGc       <  1:1413585/68‑1 (MQ=255)

                                                    caACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGc       <  1:2237393/68‑1 (MQ=255)

                                                        cGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAg  <  1:884316/69‑1 (MQ=255)

GATCAGACCTTCTTTCGGCGCGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAG  >  minE/1970264‑1970388

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