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	852,069	A→T	43.8%	T183T (ACT→ACA)	yciC ←	predicted inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	852,069	0	A	T	43.8%	18.4 / 67.2	64	T183T (ACT→ACA)	yciC	predicted inner membrane protein
Reads supporting (aligned to +/- strand): ref base A (14/22); new base T (16/12); total (30/34)
Fisher's exact test for biased strand distribution p-value = 2.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

AGCAACAGTGTTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTACCAACATCACC  >  minE/852004‑852132

agcaACAGTGTTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCAAGTc                                                              <  1:4166/69‑1 (MQ=255)

agcaACAGTCTTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCAAGTc                                                              <  1:2104421/69‑1 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCTGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:3292728/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:2932855/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:2405930/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:2227986/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:2429076/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:1013048/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:2985050/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:1716052/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:1706863/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:447148/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:1497766/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:669684/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:2894743/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:748712/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:79458/1‑69 (MQ=255)

         gtTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATa                                                     >  1:1107003/1‑69 (MQ=255)

                      aCCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCAAGTc                                                              <  1:490880/47‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCTTATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:2944542/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:2943326/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:266912/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:3158779/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:3293038/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:2338346/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:2334521/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:2143226/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:3353718/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:3432548/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:178718/69‑1 (MQ=255)

                        cAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCATGTCAGCCGCATACTGCTACGCATCGAg                                      <  1:689122/69‑1 (MQ=255)

                                  cTGCGGGTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACg                             >  1:3181978/1‑68 (MQ=255)

                                  cTGCGGGTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACg                             >  1:2425057/1‑68 (MQ=255)

                                  cTGCGGGTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACg                             >  1:2581054/1‑68 (MQ=255)

                                       ggTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCa                         >  1:3146319/1‑67 (MQ=255)

                                       ggTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCAtt                       >  1:838443/1‑69 (MQ=255)

                                       ggTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCAtt                       >  1:1092890/1‑69 (MQ=255)

                                       ggTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCAtt                       >  1:894237/1‑69 (MQ=255)

                                       ggTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCAt                        >  1:2595737/1‑68 (MQ=255)

                                       ggTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCAt                        >  1:2590017/1‑68 (MQ=255)

                                       ggTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCAAtt                       >  1:883081/1‑69 (MQ=255)

                                       ggTCCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCAtt                       >  1:3265526/1‑69 (MQ=255)

                                                   cGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACTCCCATTTTGTCCTGTAcc           <  1:457813/69‑1 (MQ=255)

                                                   cGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTAcc           <  1:1112714/69‑1 (MQ=255)

                                                   cGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTAcc           <  1:834592/69‑1 (MQ=255)

                                                   cGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTAcc           <  1:1998/69‑1 (MQ=255)

                                                   cGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTAcc           <  1:1641548/69‑1 (MQ=255)

                                                         ttCGCCCAAGTCGGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:2417502/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:1019897/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:2949904/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:77130/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:1407184/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:1413698/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:163169/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:2122409/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:2363206/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:2442998/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTg               <  1:2975711/59‑1 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTACCAACAt      >  1:3163621/1‑68 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTACCAACATc     >  1:2123969/1‑69 (MQ=255)

                                                         ttCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTACCAACATc     >  1:1385614/1‑69 (MQ=255)

                                                             cccAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTACCAACATCAcc  <  1:1604994/68‑1 (MQ=255)

                                                             cccAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTACCAACATCAcc  <  1:1418488/68‑1 (MQ=255)

                                                             cccAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTACCAACATCAcc  <  1:2699143/68‑1 (MQ=255)

AGCAACAGTGTTTTTGCCAGCAACCAGCTCAGTACTGCGGGTGCCACCAGACGCATATTCGCCCAAGTCAGCCGCATACTGCTACGCATCGAGGCAAAAACGCCCATTTTGTCCTGTACCAACATCACC  >  minE/852004‑852132

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