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	1,477,742	T→A	42.5%	A274A (GCA→GCT)	glpQ ←	periplasmic glycerophosphodiester phosphodiesterase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,477,742	0	T	A	42.5%	30.9 / 74.1	73	A274A (GCA→GCT)	glpQ	periplasmic glycerophosphodiester phosphodiesterase
Reads supporting (aligned to +/- strand): ref base T (24/18); new base A (7/24); total (31/42)
Fisher's exact test for biased strand distribution p-value = 4.10e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.31e-01

GTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCT  >  minE/1477678‑1477810

gTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCa                                                                   <  1:1282978/68‑1 (MQ=255)

 tttGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCata                                                                 <  1:1069397/69‑1 (MQ=255)

 tttGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCata                                                                 <  1:363784/69‑1 (MQ=255)

 tttGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCata                                                                 <  1:3293239/69‑1 (MQ=255)

 tttGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCata                                                                 <  1:407299/69‑1 (MQ=255)

 tttGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCata                                                                 <  1:2819627/69‑1 (MQ=255)

 tttGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCata                                                                 <  1:2625841/69‑1 (MQ=255)

 tttGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCata                                                                 <  1:2571160/69‑1 (MQ=255)

 tttGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCata                                                                 <  1:2425371/69‑1 (MQ=255)

 tttGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCata                                                                 <  1:1501200/69‑1 (MQ=255)

  ttGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCata                                                                 <  1:246037/68‑1 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:1499622/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:3320453/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:1307939/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:2524522/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:2814286/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:2273946/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:2913420/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:2963051/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:930370/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:3135266/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:1638131/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:160781/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGcc                                                          >  1:1546586/1‑69 (MQ=255)

        ttACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCAACTGCATATTCCGcc                                                          >  1:1941210/1‑69 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTa                                  <  1:3416803/68‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTa                                  <  1:383906/68‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTa                                  <  1:99112/68‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTa                                  <  1:570188/68‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTa                                  <  1:415442/68‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTa                                  <  1:502485/68‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:3267937/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:3202129/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:2661374/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:418924/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:3181178/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:3163364/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:1157554/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:1070136/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:3105578/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:1874985/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:1528880/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:1556969/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:3419559/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:1592038/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:1790342/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:733512/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:1940856/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:3330118/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:2182166/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:1373445/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:445771/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:2441774/50‑1 (MQ=255)

                                 tcaaCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:2560132/50‑1 (MQ=255)

                                  caaCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTa                                  <  1:2982019/67‑1 (MQ=255)

                                    aCATATGGTAATCCGGACCAATACCATCAGCATATTCCGCCACCTGt                                                    <  1:1671921/47‑1 (MQ=255)

                                                ccGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGt                  >  1:419183/1‑69 (MQ=255)

                                                          aCCATCAGCATATTCCGCCACCTGTTTCATAGCCCCCGGCTTAAACATCCAGTCGTAATTGTAATTaa         >  1:1476077/1‑68 (MQ=255)

                                                          aCCATCAGCATATTCCGCCACCTGTTTCATAGCCCCCGGCTTAAACATCCAGTCGTAATTGTAATTaa         >  1:1371284/1‑68 (MQ=255)

                                                          aCCATCAGCATATTCCGCCACCTGTTTCATAGCCCCCGGCTTAAACATCCAGTCGTAATTGTAATTaa         >  1:201654/1‑68 (MQ=255)

                                                          aCCATCAGCATATTCCGCCACCTGTTTCATAGCCCCCGGCTTAAACATCCAGTCGTAATTGTAATTaa         >  1:1750164/1‑68 (MQ=255)

                                                          aCCATCAGCATATTCCGCCACCTGTTTCATAGCCCCCGGCTTAAACATCCAGTCGTAATTGTAATTaa         >  1:1569752/1‑68 (MQ=255)

                                                          aCCATCAGCATATTCCGCCACCTGTTTCATAGCCCCCGGCTTAAACATCCAGTCGTAATTGTAATTa          >  1:2890069/1‑67 (MQ=255)

                                                          aCCATCAGCATATTCCGCCACCTGTTTCATAGCCCCCGGCTTAAACATCCAGTCGTAATTGTAATTa          >  1:692904/1‑67 (MQ=255)

                                                           ccATCTGCATATTCCGCCACCTGTTTCATGGCTCCCGGCTTAAACATCCAGTCGTAGTTGTAATTAAc        >  1:2657078/1‑68 (MQ=255)

                                                           ccATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTaa         >  1:3260203/1‑67 (MQ=255)

                                                           ccATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTaa         >  1:1072106/1‑67 (MQ=255)

                                                           ccATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTaa         >  1:939010/1‑67 (MQ=255)

                                                           ccATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTaa         >  1:1702641/1‑67 (MQ=255)

                                                           ccATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTaa         >  1:762760/1‑67 (MQ=255)

                                                           ccATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTaa         >  1:1961863/1‑67 (MQ=255)

                                                           ccATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTaa         >  1:529474/1‑67 (MQ=255)

                                                           ccATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTaa         >  1:3382074/1‑67 (MQ=255)

                                                                tGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATcc                           >  1:2260928/1‑44 (MQ=255)

                                                                tGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATcc                           >  1:102375/1‑44 (MQ=255)

                                                                tGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATcc                           >  1:2835395/1‑44 (MQ=255)

                                                                tGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGt               >  1:2432103/1‑56 (MQ=255)

                                                                tGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGt               >  1:1802215/1‑56 (MQ=255)

                                                                tGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGt               <  1:997206/56‑1 (MQ=255)

                                                                tGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCt  >  1:1919060/1‑69 (MQ=255)

                                                                tGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCt  >  1:2680371/1‑69 (MQ=255)

                                                                tGCATAGTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATc                            >  1:437041/1‑43 (MQ=255)

GTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCT  >  minE/1477678‑1477810

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A