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	1,807,025	G→C	61.1%	S415S (TCG→TCC)	emrB →	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,807,025	0	G	C	61.1%	33.4 / 46.5	54	S415S (TCG→TCC)	emrB	multidrug efflux system protein
Reads supporting (aligned to +/- strand): ref base G (3/18); new base C (16/17); total (19/35)
Fisher's exact test for biased strand distribution p-value = 1.81e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCC  >  minE/1806957‑1807093

gAACGACTGGCGGCGGCATCGAGCCTCTCTAAC‑TTACGCGAACGCTGGCGGGGTCTATCGGCACGTCg                                                                      <  1:3178690/68‑1 (MQ=255)

  aCGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGAt                                                                    >  1:250854/1‑69 (MQ=255)

  aCGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGAt                                                                    >  1:2037661/1‑69 (MQ=255)

  aCGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGAt                                                                    >  1:535836/1‑69 (MQ=255)

     aCTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAAc                                                                 <  1:1820569/69‑1 (MQ=255)

                                cTTTACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTc                                      <  1:1215978/69‑1 (MQ=255)

                                cTTTACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTc                                      <  1:3225856/69‑1 (MQ=255)

                                cTTTACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATCTGGACTAACCGCGAGTc                                      <  1:2089580/69‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTGTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:1888811/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTGTCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTc                                      <  1:2692055/68‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:944262/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:2525767/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:2978917/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:3045915/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:1699383/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:3136224/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:411410/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:460181/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:1459773/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:740045/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:1312219/59‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTc                                      <  1:857651/68‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTc                                      <  1:1024930/68‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTc                                      <  1:1656981/68‑1 (MQ=255)

                                 tttACGCGAACGCTGGCGGGGGCTATCGGTACGTCCATAACGACGACGATGTGGACTaa                                               <  1:2701225/59‑1 (MQ=255)

                                  ttACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGa                                    <  1:987755/69‑1 (MQ=255)

                                  ttACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGa                                    <  1:1672084/69‑1 (MQ=255)

                                       ctaaCGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc                               <  1:3400964/67‑1 (MQ=255)

                                       cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc                               <  1:24848/69‑1 (MQ=255)

                                       cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc                               <  1:3321490/69‑1 (MQ=255)

                                       cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc                               <  1:3172098/69‑1 (MQ=255)

                                       cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc                               <  1:2471695/69‑1 (MQ=255)

                                       cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc                               <  1:3000907/69‑1 (MQ=255)

                                       cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc                               <  1:2770848/69‑1 (MQ=255)

                                       cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc                               <  1:2727667/69‑1 (MQ=255)

                                        gAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc                               <  1:1097507/68‑1 (MQ=255)

                                         aaCGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCa                             <  1:2053085/69‑1 (MQ=255)

                                            gCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTc                                      <  1:2305795/57‑1 (MQ=255)

                                                     gTCTATCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTc                                      <  1:1507087/48‑1 (MQ=25)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGt                     >  1:1462554/1‑60 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:677363/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:54483/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:1454930/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:1412986/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:410887/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:1400453/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:1688002/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:3280266/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:1685279/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:3080239/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:3021388/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:2034562/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat            >  1:2046910/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTAGACCGaat            >  1:182287/1‑67 (MQ=255)

                                                          tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTAAGTTGACCGaat            >  1:1736555/1‑67 (MQ=255)

                                                                    gATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAAccc  >  1:2913360/1‑69 (MQ=255)

                                                                    gATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAAccc  >  1:2901747/1‑69 (MQ=255)

                                                                    gATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAAccc  >  1:2509535/1‑69 (MQ=255)

                                                                    gATAACCACGACCATGTCGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAAccc  >  1:1010062/1‑69 (MQ=255)

GAACGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCC  >  minE/1806957‑1807093

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