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	2,239,232	A→G	27.4%	T410T (ACT→ACC)	zraS ←	sensory histidine kinase in two‑component regulatory system with ZraR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,239,232	0	A	G	27.4%	97.0 / 37.0	91	T410T (ACT→ACC)	zraS	sensory histidine kinase in two‑component regulatory system with ZraR
Reads supporting (aligned to +/- strand): ref base A (15/51); new base G (16/9); total (31/60)
Fisher's exact test for biased strand distribution p-value = 3.98e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.42e-01

ACAATATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGATT  >  minE/2239170‑2239292

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGat                                                         <  1:3405048/68‑2 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:994007/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:2590730/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:2566016/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:2310462/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:2262154/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:2034923/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:3215300/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:1874527/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:1794765/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:1789471/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:3377209/68‑1 (MQ=255)

acaaTATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:1393081/68‑1 (MQ=255)

        atGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGaa                                                         <  1:552182/60‑1 (MQ=255)

               aCCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGa                                         <  1:484226/69‑1 (MQ=255)

               aCCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGa                                         <  1:1295647/69‑1 (MQ=255)

               aCCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGa                                         <  1:3357399/69‑1 (MQ=255)

                        cccAGTCCGGTGCCTTCGGCTTTGGTGGTGAAGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCa                                <  1:1470643/69‑1 (MQ=255)

                        cccAGTCCGGTGCCTTCGGCTTTGGTGGTGAAGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCa                                <  1:1504753/69‑1 (MQ=255)

                        cccAGTCCGGTGCCTTCGGCTTTGGTGGTGAAGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCa                                <  1:2298968/69‑1 (MQ=255)

                        cccAGTCCGGTGCCTTCGGCTTTGGTGGTGAAGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCa                                <  1:719838/69‑1 (MQ=255)

                        cccAGTCCGGTGCCTTCGGCTTTGGTGGTGAAGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCa                                <  1:2755895/69‑1 (MQ=255)

                        cccAGTCCGGTGCCTTCGGCTTTGGTGGTGAAGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCa                                <  1:818068/69‑1 (MQ=255)

                        cccAGTCCGGTGCCTTCGGCTTTGGTGGTGAAGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCa                                <  1:814110/69‑1 (MQ=255)

                        cccAGTCCGGTGCCTTCGGCTTTGGTGGTGAAGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCa                                <  1:124295/69‑1 (MQ=255)

                        cccAGTCCGGTGCCTTCGGCTTTGGTGGTGAAGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCa                                <  1:3331334/69‑1 (MQ=255)

                           aaTCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAAtt                             <  1:197722/69‑1 (MQ=255)

                           aaTCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAAtt                             <  1:2682431/69‑1 (MQ=255)

                           aaTCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAAtt                             <  1:2082581/69‑1 (MQ=255)

                           aaTCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAAtt                             <  1:3258418/69‑1 (MQ=255)

                           aaTCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAAtt                             <  1:1795945/69‑1 (MQ=255)

                           aaTCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAAtt                             <  1:1547254/69‑1 (MQ=255)

                                ggTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGa                                         <  1:2459731/52‑1 (MQ=255)

                                            tttAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGt            <  1:1911096/69‑1 (MQ=255)

                                            tttAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGt            <  1:2633865/69‑1 (MQ=255)

                                            tttAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGt            <  1:954625/69‑1 (MQ=255)

                                            tttAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGt            <  1:3419004/69‑1 (MQ=255)

                                            tttAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGt            <  1:2742163/69‑1 (MQ=255)

                                            tttAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGt            <  1:3365288/69‑1 (MQ=255)

                                            tttAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGt            <  1:1244592/69‑1 (MQ=255)

                                            tttAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGt            <  1:1998670/69‑1 (MQ=255)

                                                     gAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAt   >  1:3100232/1‑69 (MQ=255)

                                                     gAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAt   >  1:1132016/1‑69 (MQ=255)

                                                     gAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAt   >  1:1214188/1‑69 (MQ=255)

                                                     gAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAt   >  1:2619373/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:788706/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:2905332/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:2960404/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:2696343/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:2390231/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:324669/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:2661150/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:1061595/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:1286296/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:1546477/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:1608634/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:1876252/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:1937268/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCCGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:229783/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATCAGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:519619/1‑69 (MQ=255)

                                                      aaGTACGGGGTGAAGATGGCTTCAAGCTGATACGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGAtt  >  1:120724/1‑69 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:738368/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        >  1:52403/1‑40 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:1338777/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:559674/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        >  1:7101/1‑40 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:71287/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:2654470/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:2327793/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:755623/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:1249156/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:1195805/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:848932/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:936549/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:1087558/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:1068400/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:2796513/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        >  1:439393/1‑40 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        >  1:1622281/1‑40 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:162323/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        >  1:1624298/1‑40 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        >  1:1788508/1‑40 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:2290870/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        >  1:18820/1‑40 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:1905160/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:2779903/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        >  1:2215267/1‑40 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        >  1:2221247/1‑40 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCtt                        <  1:2799425/40‑1 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCt                         >  1:47001/1‑39 (MQ=255)

                                                             gAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCt                         >  1:2127715/1‑39 (MQ=255)

ACAATATTATGCACGACCGCCAGCCCCAATCCGGTGCCTTCGGCTTTAGTGGTGAAGTACGGAGTGAAGATGGCATCAAGCTGATCTGCCGCAATTCCCTTACCGCTGTCGGTAACGCTGATT  >  minE/2239170‑2239292

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