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	2,260,636	T→C	26.7%	K169K (AAA→AAG)	rpoB ←	RNA polymerase, beta subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,260,636	0	T	C	26.7%	89.7 / 31.8	82	K169K (AAA→AAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand): ref base T (38/22); new base C (3/19); total (41/41)
Fisher's exact test for biased strand distribution p-value = 1.12e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACGCCCGGACTAC  >  minE/2260572‑2260691

tCGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTa                                                      <  1:479763/68‑1 (MQ=255)

 cGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGTTACGCGCGTTATACAGCACTTTAc                                                     >  1:2984454/1‑68 (MQ=255)

 cGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTa                                                      <  1:2858908/67‑1 (MQ=255)

 cGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTAc                                                     >  1:2363534/1‑68 (MQ=255)

 cGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTAc                                                     >  1:2071094/1‑68 (MQ=255)

 cGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTAc                                                     >  1:2010986/1‑68 (MQ=255)

 cGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTAc                                                     >  1:1718903/1‑68 (MQ=255)

 cGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTAc                                                     >  1:1416518/1‑68 (MQ=255)

 cGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTAc                                                     >  1:452142/1‑68 (MQ=255)

 cGGATCGAATTCGAAGTCCAGCCAGGAACCA‑GGTAAGGGATGATACGAGCGTTATACAGCACTTTAcc                                                    >  1:1913209/1‑68 (MQ=255)

     tCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCg                                                  >  1:1753979/1‑67 (MQ=255)

     tCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCg                                                  >  1:3080045/1‑67 (MQ=255)

      cGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAag                                               <  1:2266495/69‑1 (MQ=255)

      cGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAag                                               <  1:2036955/69‑1 (MQ=255)

      cGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAag                                               <  1:1134619/69‑1 (MQ=255)

      cGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAag                                               <  1:829252/69‑1 (MQ=255)

      cGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAag                                               <  1:1533564/69‑1 (MQ=255)

      cGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAag                                               <  1:3166657/69‑1 (MQ=255)

                 tCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTa                                    >  1:2893758/1‑69 (MQ=255)

                 tCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTa                                    >  1:3143648/1‑69 (MQ=255)

                 tCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTa                                    >  1:71415/1‑69 (MQ=255)

                 tCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTa                                    >  1:249777/1‑69 (MQ=255)

                 tCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTa                                    >  1:2767399/1‑69 (MQ=255)

                   cagccagGAACCACGGTAAGGGATGATGCGCGCGTTATACAGCACCTTACCCg                                                  >  1:145575/1‑53 (MQ=255)

                   cagccagGAACCACGGTAAGGGATGATGCGCGCGTTATACAGCACCTTACCCg                                                  >  1:786393/1‑53 (MQ=255)

                   cagccagGAACCACGGTAAGGGATGATGCGCGCGTTATACAGCACCTTACCCg                                                  >  1:2823206/1‑53 (MQ=255)

                   cagccagGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTAcc                                  >  1:2843753/1‑69 (MQ=255)

                   cagccagGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTAcc                                  >  1:1879736/1‑69 (MQ=255)

                   cagccagGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTAcc                                  >  1:3240412/1‑69 (MQ=255)

                   cagccagGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTAcc                                  >  1:1944012/1‑69 (MQ=255)

                   cagccagGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTAcc                                  >  1:2785905/1‑69 (MQ=255)

                           aaCCTCGGTAAGGGATGATTCGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCgg                          <  1:3341872/69‑1 (MQ=255)

                           aaCCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCgg                          <  1:953074/69‑1 (MQ=255)

                           aaCCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCgg                          <  1:83697/69‑1 (MQ=255)

                           aaCCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCgg                          <  1:2836125/69‑1 (MQ=255)

                           aaCCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCgg                          >  1:534293/1‑69 (MQ=255)

                           aaCCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCgg                          <  1:2459707/69‑1 (MQ=255)

                           aaCCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCgg                          <  1:1050198/69‑1 (MQ=255)

                           aaCCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCgg                          >  1:1626785/1‑69 (MQ=255)

                           aaCCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCgg                          <  1:2257576/69‑1 (MQ=255)

                                cGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGt                       >  1:1428141/1‑67 (MQ=255)

                                cGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGt                       >  1:312213/1‑67 (MQ=255)

                                cGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGt                       >  1:308086/1‑67 (MQ=255)

                                cGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGt                       >  1:1686972/1‑67 (MQ=255)

                                cGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGt                       >  1:1803914/1‑67 (MQ=255)

                                cGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGt                       >  1:2007407/1‑67 (MQ=255)

                                cGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCAAAGAGTGGGTTTTACCTTTGTCgg                          <  1:1447147/64‑1 (MQ=255)

                                cGGTAAGGGATGATACGCGCGTTATAAAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGt                       >  1:2389986/1‑67 (MQ=255)

                                         atgatACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACg            <  1:1276358/69‑1 (MQ=255)

                                         atgatACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACg            <  1:1047991/69‑1 (MQ=255)

                                         atgatACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACg            <  1:1263595/69‑1 (MQ=255)

                                         atgatACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTATACCTTTGTCGGAGTCAAAGAAGACg            <  1:1694543/69‑1 (MQ=255)

                                            atACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACGcc          >  1:492847/1‑68 (MQ=255)

                                            atACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACGcc          >  1:3097242/1‑68 (MQ=255)

                                             tACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACGCCCg        >  1:2321472/1‑69 (MQ=255)

                                              aCGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACGCCCg        <  1:536091/68‑1 (MQ=255)

                                               cgcgcgTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACGCCCgg       >  1:2168724/1‑68 (MQ=255)

                                               cgcgcgTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACGCCCgg       >  1:829868/1‑68 (MQ=255)

                                               cgcgcgTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACGCCCgg       >  1:3318697/1‑68 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTc                            <  1:1290029/40‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTc                            <  1:227135/40‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:570548/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:1231644/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:1209283/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:1111288/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:948195/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:476496/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:213005/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:384846/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:1350746/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:3282639/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:1411543/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:3193621/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:2312610/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:2591580/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:1788678/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:1837464/43‑1 (MQ=255)

                                                      tataCAGCACCTTACCCGAAGAGTGGGTTTTACCTTTGTCGGa                         <  1:2794682/43‑1 (MQ=255)

                                                            gCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAaagaa                >  1:3320199/1‑46 (MQ=255)

                                                            gCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAaagaa                >  1:796255/1‑46 (MQ=255)

                                                            gCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAaagaa                >  1:1137169/1‑46 (MQ=255)

                                                            gCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACGCCCGGACTAc  <  1:2879868/60‑1 (MQ=255)

TCGGATCGAATTCGAAGTCCAGCCAGGAACCACGGTAAGGGATGATACGCGCGTTATACAGCACTTTACCCGAAGAGTGGGTTTTACCTTTGTCGGAGTCAAAGAAGACGCCCGGACTAC  >  minE/2260572‑2260691

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