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 I1 R1	67	31.4	1402038	96.1%	1347358	109.5

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%	106.1 / NA	32	T275I (ACC→ATC)	lptF	lipopolysaccharide export ABC permease
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (16/16); total (16/16)

ATCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCACCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAC  >  NC_000913/4486906‑4487174

aTCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCgt                                                                                                                                    >  1:229739/1‑139 (MQ=255)

                 cACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTa                                                                                                                   >  2:36180/1‑139 (MQ=255)

                    cAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATgg                                                                                                                >  2:172588/1‑139 (MQ=255)

                       gCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTatga                                                                                                                            >  2:302963/1‑124 (MQ=255)

                       gCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTatga                                                                                                                            <  1:302963/124‑1 (MQ=255)

                                  cGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGc                                                                                                  <  2:229739/139‑1 (MQ=255)

                                            gATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGTGTGGTTAAcc                                                                                        <  2:698953/139‑1 (MQ=255)

                                                   aCCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGTACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        <  1:243241/132‑1 (MQ=255)

                                                   aCCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGTACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        >  2:243241/1‑132 (MQ=255)

                                                   aCCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCa                                                                                 <  1:297641/139‑1 (MQ=255)

                                                   aCCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCa                                                                                 >  1:577945/1‑139 (MQ=255)

                                                           gACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGAGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGAcgcg                                                                         <  1:418395/139‑1 (MQ=255)

                                                                                  tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        >  2:63888/1‑101 (MQ=255)

                                                                                  tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAAcc                                                                                        <  1:63888/101‑1 (MQ=255)

                                                                                  tGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtg                                                  >  1:696113/1‑139 (MQ=255)

                                                                                       ccGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATgctgct                                             <  2:127439/139‑1 (MQ=255)

                                                                                          aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGt                                                                                             >  2:185451/1‑88 (MQ=255)

                                                                                          aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGt                                                                                             <  1:185451/88‑1 (MQ=255)

                                                                                          aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGAcgcg                                                                         >  1:145650/1‑108 (MQ=255)

                                                                                          aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGAcgcg                                                                         <  2:145650/108‑1 (MQ=255)

                                                                                          aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgct                                                >  2:221312/1‑133 (MQ=255)

                                                                                          aTCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgct                                                <  1:221312/133‑1 (MQ=255)

                                                                                                   gcgcAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACtttt                                 <  1:172588/139‑1 (MQ=255)

                                                                                                    cgcAGAACTGAACTGGCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTttc                                >  2:400450/1‑139 (MQ=255)

                                                                                                                 tggtgTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGt                                           <  2:246575/111‑1 (MQ=255)

                                                                                                                 tgGTGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGt                                           >  1:246575/1‑115 (MQ=255)

                                                                                                                   gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAg                                                                                                   >  1:692763/1‑57 (MQ=255)

                                                                                                                   gCGTATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAg                                                                                                   <  2:692763/57‑1 (MQ=255)

                                                                                                                      tATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgct                                                <  1:674343/105‑1 (MQ=255)

                                                                                                                      tATCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCAtgct                                                >  2:674343/1‑105 (MQ=255)

                                                                                                                        tCACGTTGGTATTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCt            >  1:132079/1‑139 (MQ=255)

                                                                                                                                  aTTCATCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAc  <  1:36180/139‑1 (MQ=255)

ATCAGGCGATCATTGGTCACCAGGCGGTGGCGCTCGACCCGAACGATACCGACCAGATGGACATGCGCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCACCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAAC  >  NC_000913/4486906‑4487174

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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