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	1,888,954	A→G	30.5%	G425G (GGT→GGC)	gudX ←	predicted glucarate dehydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,888,954	0	A	G	30.5%	75.6 / 40.6	85	G425G (GGT→GGC)	gudX	predicted glucarate dehydratase
Reads supporting (aligned to +/- strand): ref base A (20/39); new base G (12/14); total (32/53)
Fisher's exact test for biased strand distribution p-value = 3.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.93e-01

ACGGCCGAAAACGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCTGTT  >  minE/1888894‑1889018

aCGGCCGAAAACGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGcgtc                                                          <  1:1783848/69‑1 (MQ=255)

aCGGCCGAAAACGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGcgtc                                                          <  1:2975183/69‑1 (MQ=255)

aCGGCCGAAAACGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGcgtc                                                          <  1:367927/69‑1 (MQ=255)

aCGGCCGAAAACGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGcgtc                                                          <  1:2128935/69‑1 (MQ=255)

aCGGCCGAAAACGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGcgtc                                                          <  1:2776483/69‑1 (MQ=255)

aCGGCCGAAAACGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGcgtc                                                          <  1:465764/69‑1 (MQ=255)

aCGGCCGAAAACGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGcgtc                                                          <  1:628957/69‑1 (MQ=255)

 cGGCCGAAACCGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGcgtc                                                          <  1:135955/68‑1 (MQ=255)

 cGGCCGAAAACGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGcgtc                                                          <  1:1556476/68‑1 (MQ=255)

         aaCGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACgcgc                                                 <  1:2784576/69‑1 (MQ=255)

         aaCGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACgcgc                                                 <  1:335717/69‑1 (MQ=255)

         aaCGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACgcgc                                                 <  1:2374024/69‑1 (MQ=255)

          aCGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACgcgc                                                 <  1:2778802/68‑1 (MQ=255)

          aCGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACgcgc                                                 <  1:983783/68‑1 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:2165901/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:33660/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:2377502/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:2431163/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:2081963/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:321142/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:1768305/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:2980339/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:1585310/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:763659/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:140778/1‑68 (MQ=255)

                 gTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCa                                          >  1:3347690/1‑68 (MQ=255)

                 gTTTAAGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACgcgc                                                 <  1:1496945/61‑1 (MQ=255)

                  tttACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGcgtc                                                          <  1:1890572/51‑1 (MQ=255)

                    tACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGc                                       >  1:484785/1‑68 (MQ=255)

                    tACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCa                                      >  1:3311593/1‑69 (MQ=255)

                    tACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCa                                      >  1:3297480/1‑69 (MQ=255)

                    tACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCa                                      >  1:1236365/1‑69 (MQ=255)

                          cAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGtt                                <  1:2842158/69‑1 (MQ=255)

                          cAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGtt                                <  1:3371104/69‑1 (MQ=255)

                          cAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGtt                                <  1:2179796/69‑1 (MQ=255)

                          cAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGtt                                <  1:367121/69‑1 (MQ=255)

                          cAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGtt                                <  1:1517549/69‑1 (MQ=255)

                          cAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGtt                                <  1:1016616/69‑1 (MQ=255)

                             aGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTta                              <  1:2365232/68‑1 (MQ=255)

                             aGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTta                              <  1:2162310/68‑1 (MQ=255)

                             aGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTta                              <  1:1874146/68‑1 (MQ=255)

                             aGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTta                              <  1:1693052/68‑1 (MQ=255)

                             aGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTta                              <  1:2958425/68‑1 (MQ=255)

                                     ccGGGTATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:1449074/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:995078/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:312088/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:3042401/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:457425/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:854354/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:1662043/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:1929034/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:2523162/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:2196358/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:2304509/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:1571333/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:1625890/69‑1 (MQ=255)

                                     ccGGGGATCAGGTACTGCATCGGGCCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCa                     <  1:1612306/69‑1 (MQ=255)

                                       ggggATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCAtg                   <  1:891500/69‑1 (MQ=255)

                                          gATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGc                >  1:945982/1‑69 (MQ=255)

                                           aTCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTta                              <  1:1665057/54‑1 (MQ=255)

                                            tCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCt              >  1:234320/1‑69 (MQ=255)

                                            tCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCt              >  1:3123872/1‑69 (MQ=255)

                                            tCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCt              >  1:2296560/1‑69 (MQ=255)

                                            tCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCt              >  1:3105947/1‑69 (MQ=255)

                                            tCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCt              >  1:2561924/1‑69 (MQ=255)

                                            tCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAAACGTTTATAGGCCTCATGTGCCt              >  1:3222766/1‑69 (MQ=255)

                                                 tACTGCATCGGACCTGCGTCGTTACGCGCACCGCCa                                          >  1:2856930/1‑36 (MQ=255)

                                                 tACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGt         >  1:704854/1‑69 (MQ=255)

                                                 tACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGt         >  1:1643883/1‑69 (MQ=255)

                                                 tACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGt         >  1:1351496/1‑69 (MQ=255)

                                                 tACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGt         >  1:2482370/1‑69 (MQ=255)

                                                  aCTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTa        <  1:938409/69‑1 (MQ=255)

                                                  aCTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTa        <  1:2991280/69‑1 (MQ=255)

                                                     gCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCt     <  1:1906194/69‑1 (MQ=255)

                                                     gCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCt     <  1:1959855/69‑1 (MQ=255)

                                                     gCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCt     <  1:2448448/69‑1 (MQ=255)

                                                     gCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCt     <  1:3187971/69‑1 (MQ=255)

                                                     gCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCt     <  1:842683/69‑1 (MQ=255)

                                                     gCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCt     <  1:1378434/69‑1 (MQ=255)

                                                     gCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGACTCATGTGCCTTTTGTACCt     <  1:3163465/69‑1 (MQ=255)

                                                     gCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGACTCATGTGCCTTTTGTACCt     <  1:3159344/69‑1 (MQ=255)

                                                          ggACCTGCGTCGTTACGCGCCCCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCTGtt  >  1:592701/1‑67 (MQ=255)

                                                          ggACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCTGtt  >  1:665245/1‑67 (MQ=255)

                                                          ggACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCTGtt  >  1:1522124/1‑67 (MQ=255)

                                                          ggACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCTGtt  >  1:2976323/1‑67 (MQ=255)

ACGGCCGAAAACGGGACGTTTACGGTCAAAGGTCCAGCCGGGGATCAGGTACTGCATCGGACCTGCGTCGTTACGCGCACCGCCAGGCAGACGTTTATAGGCCTCATGTGCCTTTTGTACCTGTT  >  minE/1888894‑1889018

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A