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	2,827,078	G→A	28.2%	intergenic (‑60/+56)	cutA ← / ← dcuA	copper binding protein, copper sensitivity/C4‑dicarboxylate antiporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,827,078	0	G	A	28.2%	54.8 / 19.4	53	intergenic (‑60/+56)	cutA/dcuA	copper binding protein, copper sensitivity/C4‑dicarboxylate antiporter
Reads supporting (aligned to +/- strand): ref base G (10/28); new base A (10/5); total (20/33)
Fisher's exact test for biased strand distribution p-value = 1.10e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.85e-01

AAGCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAG  >  minE/2827013‑2827139

aaGCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAg                                                            <  1:2685061/69‑1 (MQ=255)

aaGCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAg                                                            <  1:463048/69‑1 (MQ=255)

aaGCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAg                                                            <  1:460477/69‑1 (MQ=255)

aaGCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAg                                                            <  1:1441705/69‑1 (MQ=255)

aaGCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAg                                                            <  1:2240401/69‑1 (MQ=255)

aaGCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAg                                                            <  1:422090/69‑1 (MQ=255)

aaGCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAg                                                            <  1:2454026/69‑1 (MQ=255)

  gCATAAATACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAgg                                                           <  1:1922428/68‑1 (MQ=255)

  gCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGTGAGGTCACTATACAACGGACGGGGGAAgg                                                           <  1:465936/68‑1 (MQ=255)

  gCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAgg                                                           <  1:2494366/68‑1 (MQ=255)

  gCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAgg                                                           <  1:264116/68‑1 (MQ=255)

  gCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAgg                                                           <  1:418747/68‑1 (MQ=255)

   cATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAgg                                                           <  1:2229390/67‑1 (MQ=255)

       aaCACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAGGATGTTa                                                     >  1:3254811/1‑69 (MQ=255)

       aaCACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAGGATGTTa                                                     >  1:518027/1‑69 (MQ=255)

       aaCACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAGGATGTTa                                                     >  1:2411033/1‑69 (MQ=255)

       aaCACCTCGCAAGAACAGATGGAACCGCAAGAGAGA‑GTCACTATACAACGGACGGGGGAAGGATGTTAg                                                    >  1:2424705/1‑69 (MQ=255)

                       aGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAg                                                            >  1:409343/1‑46 (MQ=255)

                       aGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAg                                                            >  1:2791993/1‑46 (MQ=255)

                       aGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAg                                                            >  1:937695/1‑46 (MQ=255)

                       aGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAg                                                            >  1:437604/1‑46 (MQ=255)

                       aGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAg                                                            >  1:474003/1‑46 (MQ=255)

                       aGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAg                                                            >  1:922599/1‑46 (MQ=255)

                       aGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAg                                                            >  1:1141970/1‑46 (MQ=255)

                       aGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAg                                                            >  1:1301787/1‑46 (MQ=255)

                       aGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAg                                                            >  1:133351/1‑46 (MQ=255)

                       aGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAg                                                            >  1:1798610/1‑46 (MQ=255)

                          tGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAGGATGTTa                                                     <  1:2301961/50‑1 (MQ=255)

                          tGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAGGATGTTa                                                     <  1:1050589/50‑1 (MQ=255)

                          tGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAGGATGTTa                                                     <  1:2730275/50‑1 (MQ=255)

                          tGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAGGATGTTa                                                     <  1:157749/50‑1 (MQ=255)

                          tGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGAAAGGATGTTa                                                     <  1:1793003/50‑1 (MQ=255)

                           ggAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAgg                                                           <  1:1339661/43‑1 (MQ=255)

                               ccGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCg                             <  1:1837614/69‑1 (MQ=255)

                               ccGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCg                             <  1:436532/69‑1 (MQ=255)

                               ccGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAGGATGTTAGTCGGCCGGAAAGAAAGCGGGGCg                             <  1:3307613/69‑1 (MQ=255)

                                 gCAAGAGAGAGGTCACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTg                           <  1:2073600/69‑1 (MQ=255)

                                 gCAAGAGAGAGGTCACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTg                           <  1:294607/69‑1 (MQ=255)

                                             tCACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGa               <  1:1988439/69‑1 (MQ=255)

                                              cACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAAGGCCCCGCGa               >  1:2956562/1‑68 (MQ=255)

                                              cACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGa               >  1:3384253/1‑68 (MQ=255)

                                              cACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGa               >  1:2823912/1‑68 (MQ=255)

                                              cACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGa               <  1:273794/68‑1 (MQ=255)

                                              cACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGa               >  1:1892497/1‑68 (MQ=255)

                                               aCTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGAtt             >  1:1180575/1‑69 (MQ=255)

                                               aCTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGAtt             >  1:1152129/1‑69 (MQ=255)

                                                 tataCAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTg            <  1:2973109/68‑1 (MQ=255)

                                                 tataCAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTg            <  1:201300/68‑1 (MQ=255)

                                                        cggccggGGGAAGGATGTTAGTCGGCGGGAAAGAACGCGGGGCGTGAACGCCCCGCGATTg            <  1:3235957/61‑1 (MQ=255)

                                                          gacggGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAg  <  1:1824026/69‑1 (MQ=255)

                                                          gacggGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAg  <  1:1466991/69‑1 (MQ=255)

                                                           acggGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAg  <  1:3405454/68‑1 (MQ=255)

                                                           acggGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAg  <  1:552107/68‑1 (MQ=255)

AAGCATAAACACCTCGCAAGAACAGATGGAACCGCAAGAGAGAGGTCACTATACAACGGACGGGGGAAGGATGTTAGTCGGCGGGAAAGAAAGCGGGGCGTGAACGCCCCGCGATTGATCATTACAG  >  minE/2827013‑2827139

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