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	1,581,564	T→G	55.4%	A557A (GCA→GCC)	ligA ←	DNA ligase, NAD(+)‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,581,564	0	T	G	55.4%	37.6 / 68.4	76	A557A (GCA→GCC)	ligA	DNA ligase, NAD(+)‑dependent
Reads supporting (aligned to +/- strand): ref base T (5/29); new base G (13/29); total (18/58)
Fisher's exact test for biased strand distribution p-value = 1.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGGCTTCCAGCGCTTCCAG  >  minE/1581503‑1581632

ccAACAGCTCGCTGATGACATTGCGGTT‑CTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:2936727/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACTTTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:3264611/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:3071413/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:1869190/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:1782036/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:1644199/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:3282573/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:1570981/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:3247938/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:2796848/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:1187009/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:3013635/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:2790233/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:2821342/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:2871174/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:2872228/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:2595254/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:3350091/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:2554458/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:345490/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:449040/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:102136/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:481145/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:588688/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:1099652/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:1915017/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:700757/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:1814563/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:1809998/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:1376153/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:704670/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:1478103/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:1562674/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:888900/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTCGGAGGCAACGAc                                                              <  1:651279/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTCGGAGGCAACGAc                                                              <  1:3142530/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTCGTGAACGTGGGAGGCAACGAc                                                              <  1:2839168/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGGGTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:390599/69‑1 (MQ=255)

 cAACAGCTCGCTGATGACATTGCGATTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:952501/69‑1 (MQ=255)

  aaCAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGAGGCAACGAc                                                              <  1:955159/68‑1 (MQ=255)

        tCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGAc                                                              <  1:1223001/62‑1 (MQ=255)

                   aTTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCa                                             <  1:730934/68‑1 (MQ=255)

                   aTTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCa                                             <  1:1289232/68‑1 (MQ=255)

                   aTTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCa                                             <  1:1980493/68‑1 (MQ=255)

                      gCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGc                                                                    >  1:1113105/1‑42 (MQ=255)

                          ttGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:837041/69‑1 (MQ=255)

                          ttGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:3319419/69‑1 (MQ=255)

                          ttGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:342166/69‑1 (MQ=255)

                          ttGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:3080980/69‑1 (MQ=255)

                          ttGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:1075091/69‑1 (MQ=255)

                          ttGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:2017440/69‑1 (MQ=255)

                          ttGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:2167746/69‑1 (MQ=255)

                          ttGCTTTCTTCGGCAAAGAAGTTATGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:934394/69‑1 (MQ=255)

                          tagCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:1899740/67‑1 (MQ=255)

                           tGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:599103/68‑1 (MQ=255)

                           tGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:2587250/68‑1 (MQ=255)

                           tGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGc                                     <  1:1606303/68‑1 (MQ=255)

                           tGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGCa                                    >  1:872338/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:831588/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:685809/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:1724011/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:738491/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:489524/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:2416576/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:2512163/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:2616740/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:3274796/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:2697358/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:3033529/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCaa                           >  1:2882275/1‑69 (MQ=255)

                                    cGGCAAAGAAGTTGTGAACGTGGGAGGCAACGACAATTCCAACATCAGGCACCTTTTGCAGCTCTTCa                            >  1:1431911/1‑68 (MQ=255)

                                        aaaGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGa                       >  1:988134/1‑69 (MQ=255)

                                            aagTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCg                   <  1:901578/69‑1 (MQ=255)

                                            aagTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCg                   <  1:3172324/69‑1 (MQ=255)

                                                 gtgAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgct                >  1:21342/1‑67 (MQ=255)

                                                 gtgAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgct                >  1:3240074/1‑67 (MQ=255)

                                                             tGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgcttccagcgcttccag  >  1:655156/1‑69 (MQ=255)

                                                             tGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgcttccagcgcttccag  >  1:1713984/1‑69 (MQ=255)

                                                             tGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgcttccagcgcttccag  >  1:573750/1‑69 (MQ=255)

                                                             tGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgcttccagcgcttccag  >  1:2538499/1‑69 (MQ=255)

                                                             tGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgcttccagcgcttccag  >  1:1671556/1‑69 (MQ=255)

                                                             tGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgcttccagcgcttccag  >  1:2545262/1‑69 (MQ=255)

                                                             tGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgcttccagcgcttccag  >  1:2578158/1‑69 (MQ=255)

                                                             tGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgcttccagcgcttccag  >  1:2778019/1‑69 (MQ=255)

                                                             tGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGgcttccagcgcttccag  <  1:1293457/69‑1 (MQ=255)

CCAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCCAACATCAGGCACCTTTTGCAGCTCTTCAATCGAAGCGGCTTCCAGCGCTTCCAG  >  minE/1581503‑1581632

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