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	2,281,337	A→G	36.2%	intergenic (‑17/‑260)	fabR ← / → sthA	DNA‑binding transcriptional repressor/pyridine nucleotide transhydrogenase, soluble

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,281,337	0	A	G	36.2%	47.5 / 48.4	80	intergenic (‑17/‑260)	fabR/sthA	DNA‑binding transcriptional repressor/pyridine nucleotide transhydrogenase, soluble
Reads supporting (aligned to +/- strand): ref base A (28/23); new base G (15/14); total (43/37)
Fisher's exact test for biased strand distribution p-value = 8.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.66e-01

TGAATCCTTGCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCTTTT  >  minE/2281273‑2281397

tGAATCCTTGCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATtg                                                           >  1:2621211/1‑68 (MQ=255)

    tCCTTGCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATtgtg                                                         <  1:548299/66‑1 (MQ=255)

    tCCTTGCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATtgtg                                                         <  1:2641310/66‑1 (MQ=255)

    tCCTTGCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATtgtg                                                         <  1:2718063/66‑1 (MQ=255)

    tCCTTGCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATtgtg                                                         <  1:2734406/66‑1 (MQ=255)

    tCCTTGCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATtgtg                                                         <  1:1636152/66‑1 (MQ=255)

         gCCAAATGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:867281/61‑1 (MQ=255)

         gCCAAAAGTACTGCTTGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:1070695/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGTCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:1958800/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTTCTCCAGTGTtgtg                                                         <  1:2779941/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:3404370/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:1973658/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:1911810/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:2644500/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:397129/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:475475/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:675879/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:1230890/61‑1 (MQ=255)

         gCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:1180640/61‑1 (MQ=255)

          ccAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTGTtgtg                                                         <  1:2411873/60‑1 (MQ=255)

              aaGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTaa                                             >  1:1121912/1‑68 (MQ=255)

              aaGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTaa                                             >  1:3410430/1‑68 (MQ=255)

              aaGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTaa                                             >  1:516387/1‑68 (MQ=255)

              aaGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTaa                                             >  1:1182580/1‑68 (MQ=255)

              aaGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTaa                                             >  1:142908/1‑68 (MQ=255)

              aaGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTa                                              >  1:2124185/1‑67 (MQ=255)

                        ggCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATaaaa                                   >  1:341288/1‑68 (MQ=255)

                           aCTATACCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACa                                 <  1:159300/67‑1 (MQ=255)

                             tataCCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             <  1:165238/69‑1 (MQ=255)

                               taCCAGAGAATGAACATACTGGATTGCTCCAGTATTGtgaatg                                                     <  1:2153472/43‑1 (MQ=255)

                               taCCAGAGAATGAACATACTGGATTGCTCCAGTATTGtgaatg                                                     <  1:65907/43‑1 (MQ=255)

                                 ccAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTAc                          >  1:2954599/1‑68 (MQ=255)

                                 ccAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTAc                          >  1:2823617/1‑68 (MQ=255)

                                 ccAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTAc                          >  1:2795863/1‑68 (MQ=255)

                                           aaCATACTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCttt               >  1:2585791/1‑69 (MQ=255)

                                           aaCATACTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCttt               >  1:1892640/1‑69 (MQ=255)

                                                aCTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             <  1:3031201/50‑1 (MQ=255)

                                                aCTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             <  1:3296107/50‑1 (MQ=255)

                                                aCTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             <  1:577586/50‑1 (MQ=255)

                                                aCTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             <  1:1299936/50‑1 (MQ=255)

                                                aCTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             <  1:209889/50‑1 (MQ=255)

                                                   ggATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGt        <  1:683687/68‑1 (MQ=255)

                                                   ggATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGt        <  1:81343/68‑1 (MQ=255)

                                                      ttGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCt     <  1:1716958/68‑1 (MQ=255)

                                                      ttGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCt     <  1:607396/68‑1 (MQ=255)

                                                      ttGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCt     <  1:1395863/68‑1 (MQ=255)

                                                      ttGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCt     <  1:2537900/68‑1 (MQ=255)

                                                      ttGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCt     <  1:1470849/68‑1 (MQ=255)

                                                      ttGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCt     <  1:2415125/68‑1 (MQ=255)

                                                      ttGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCt     <  1:3361775/68‑1 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAATGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCtt    >  1:3053060/1‑68 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCGATTCTTTGGCCGGTTCtt    >  1:282224/1‑68 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:911043/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:818236/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:2464716/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:254287/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:2589912/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:3349026/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:644365/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:1470990/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:2946208/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:1927024/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:1339253/1‑69 (MQ=255)

                                                       tGCTCCAGTGTTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCttt   >  1:535070/1‑69 (MQ=255)

                                                       tGCTCCAGTGTT‑TGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCtttt  >  1:2827884/1‑69 (MQ=255)

                                                              gTATTGTGAATGAACGGTACCGCAATAAAACATAtt                             >  1:3096398/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:2102437/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:448703/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:425305/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:1467169/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:1866580/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:2904937/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:3001872/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:3301248/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:3019136/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:2530726/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:3130228/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:3111480/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:839210/1‑36 (MQ=255)

                                                              gTATTGTGAATGAACGGTAACGCAATAAAACATAtt                             >  1:2265490/1‑36 (MQ=255)

TGAATCCTTGCCAAAAGTACTGCTGGCACTATACCAGAGAATGAACATACTGGATTGCTCCAGTATTGTGAATGAACGGTAACGCAATAAAACATATTTACTGCAATTCTTTGGCCGGTTCTTTT  >  minE/2281273‑2281397

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A