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
A12 F1 I2 R1	766	55.6	2631458	94.7%	2491990	109.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,664,096	T→C	I163T (ATA→ACA)	ynfH →	oxidoreductase, membrane subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,664,096	0	T	C	100.0%	133.6 / NA	38	I163T (ATA→ACA)	ynfH	oxidoreductase, membrane subunit
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/19); total (19/19)

TTCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAATACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGCGTCT  >  NC_000913/1663990‑1664223

ttCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTcgcg                                                                                                   <  2:1073957/139‑1 (MQ=255)

 tCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGt                                                                                                  <  2:140414/139‑1 (MQ=255)

  cGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGtt                                                                                                 <  2:661693/139‑1 (MQ=255)

   gTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTa                                                                                                >  1:296107/1‑139 (MQ=255)

   gTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTa                                                                                                <  1:300482/139‑1 (MQ=255)

        gatgatGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACAttt                                                                                           >  1:937883/1‑139 (MQ=255)

                  tGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACTGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCa                                                                                                                      <  2:859660/102‑1 (MQ=255)

                  tGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCacac                                                                                 <  1:915616/139‑1 (MQ=255)

                  tGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTAACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCa                                                                                                                      >  1:859660/1‑102 (MQ=255)

                        tATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTg                                                                           >  2:35576/1‑139 (MQ=255)

                        tATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTg                                                                           >  1:666459/1‑139 (MQ=255)

                          tCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACAttt                                                                                           >  1:217854/1‑121 (MQ=255)

                          tCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACAttt                                                                                           <  2:217854/121‑1 (MQ=255)

                             aaTCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCcatc                                                                      >  2:219108/1‑139 (MQ=255)

                                        tGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTa                                                                                                <  1:978149/102‑1 (MQ=255)

                                        tGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTa                                                                                                >  2:978149/1‑102 (MQ=255)

                                        tGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCt                                                         >  2:892484/1‑139 (MQ=255)

                                            aaCCTGGGATAACGGTTACACTACGCTGGCGTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGgcg                                                     <  2:904531/139‑1 (MQ=255)

                                                 ggCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGAt                                                <  1:219108/139‑1 (MQ=255)

                                                                 tACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTcgcg                                                                                                   <  1:622396/74‑1 (MQ=255)

                                                                 tACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTcgcg                                                                                                   >  2:622396/1‑74 (MQ=255)

                                                                  aCGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGa                               <  2:97750/139‑1 (MQ=255)

                                                                   cGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGTCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGAt                              >  1:45986/1‑139 (MQ=255)

                                                                   cGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGAt                              >  2:418966/1‑139 (MQ=255)

                                                                   cGCTGGCTTTCTTCCTGACGGT‑TTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGtt                                                                                                 <  1:12338/73‑1 (MQ=255)

                                                                   cGCTGGCTTTCTTCCTGACGGT‑TTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGtt                                                                                                 >  2:12338/1‑73 (MQ=255)

                                                                     cTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATtg                            >  1:1185099/1‑139 (MQ=255)

                                                                        gCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTc                                                          >  1:953385/1‑106 (MQ=255)

                                                                        gCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTc                                                          <  2:953385/106‑1 (MQ=255)

                                                                         cTTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGTGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGtgct                        >  2:824670/1‑139 (MQ=255)

                                                                             cttcCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGATCGCTTGTGCCggg                                   >  2:523704/1‑124 (MQ=255)

                                                                             cttcCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGATCGCTTGTGCCggg                                   <  1:523704/124‑1 (MQ=255)

                                                                                        tATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACAtt                                                                                            >  2:546722/1‑58 (MQ=255)

                                                                                        tATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACAtt                                                                                            <  1:546722/58‑1 (MQ=255)

                                                                                          ttgttgAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACca                                                                                    <  1:978169/64‑1 (MQ=255)

                                                                                          ttgttgAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACca                                                                                    >  2:978169/1‑64 (MQ=255)

                                                                                           tgttgAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGc      <  1:418966/139‑1 (MQ=255)

                                                                                                 gCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGCGTCt  <  2:296107/139‑1 (MQ=255)

TTCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCCTGACGGTATTGTTGAGCGGTCCAATACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTA‑‑GCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGCGTCT  >  NC_000913/1663990‑1664223

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A