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
A6 F1 I2 R1	67	27.9	1239648	95.3%	1181384	112.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,487,041	C→T	T275I (ACC→ATC)	lptF →	lipopolysaccharide export ABC permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,487,041	0	C	T	100.0%	124.1 / NA	36	T275I (ACC→ATC)	lptF	lipopolysaccharide export ABC permease
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (16/20); total (16/20)

ATCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCACCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAC  >  NC_000913/4486906‑4487174

aTCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCgt                                                                                                                                    >  2:399669/1‑139 (MQ=255)

        aTCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTatga                                                                                                                            >  2:54503/1‑139 (MQ=255)

          cATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTatgatg                                                                                                                          <  1:399669/139‑1 (MQ=255)

                   ccAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATg                                                                                                                 >  2:252703/1‑139 (MQ=255)

                                       cGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGt                                                                                             <  1:204751/139‑1 (MQ=255)

                                                   aCCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCa                                                                                 >  2:204533/1‑139 (MQ=255)

                                                                     caTTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        >  1:165743/1‑114 (MQ=255)

                                                                     caTTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        <  2:165743/114‑1 (MQ=255)

                                                                                  tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtg                                                  >  2:74547/1‑139 (MQ=255)

                                                                                  tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtg                                                  >  2:257478/1‑139 (MQ=255)

                                                                                  tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtg                                                  <  2:256528/139‑1 (MQ=255)

                                                                                    acacCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGAcgcg                                                                         <  2:256753/114‑1 (MQ=255)

                                                                                    acacCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGAcgcg                                                                         >  1:256753/1‑114 (MQ=255)

                                                                                     cacCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctg                                               <  1:252703/139‑1 (MQ=255)

                                                                                     cacCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctg                                               <  2:43292/139‑1 (MQ=255)

                                                                                      acCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctgc                                              <  2:459872/139‑1 (MQ=255)

                                                                                      acCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctgc                                              <  1:257478/139‑1 (MQ=255)

                                                                                          aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTa                                          >  2:199253/1‑139 (MQ=255)

                                                                                           tCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATgctgct                                             <  2:426145/135‑1 (MQ=255)

                                                                                           tCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATgctgct                                             >  1:426145/1‑135 (MQ=255)

                                                                                             gTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCt                                       <  1:504702/139‑1 (MQ=255)

                                                                                              tGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctg                                               <  2:167357/130‑1 (MQ=255)

                                                                                              tGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgctg                                               >  1:167357/1‑130 (MQ=255)

                                                                                              tGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTa                                      >  1:457525/1‑139 (MQ=255)

                                                                                               gCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGt                                                                                             >  1:315864/1‑83 (MQ=255)

                                                                                               gCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGt                                                                                             <  2:315864/83‑1 (MQ=255)

                                                                                                   gcgcAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACtttt                                 <  1:204533/139‑1 (MQ=255)

                                                                                                       aGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTttcttc                             <  2:425396/139‑1 (MQ=255)

                                                                                                        gaactgaactGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTcc                            <  1:199253/139‑1 (MQ=255)

                                                                                                                   gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        <  1:224677/68‑1 (MQ=255)

                                                                                                                   gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        >  2:224677/1‑68 (MQ=255)

                                                                                                                   gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACtttt                                 <  2:156737/123‑1 (MQ=255)

                                                                                                                   gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACtttt                                 >  1:156737/1‑123 (MQ=255)

                                                                                                                           cGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAgg                                                                               <  2:460974/69‑1 (MQ=255)

                                                                                                                           cGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAgg                                                                               >  1:460974/1‑69 (MQ=255)

                                                                                                                                  aTTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAc  <  2:457525/139‑1 (MQ=255)

ATCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCACCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAC  >  NC_000913/4486906‑4487174

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A