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
A4 F1 I2 R1	67	32.5	1435938	95.9%	1377064	112.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,595,427	A→G	pseudogene (2561/3861 nt)	yneO ←	pseudogene, AidA homolog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,595,427	0	A	G	100.0%	114.1 / NA	31	pseudogene (2561/3861 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (14/17); total (14/17)

CGCCTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTACCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGC  >  NC_000913/1595297‑1595557

cgcCTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAg                                                                                                                            >  1:271745/1‑139 (MQ=255)

       aCCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGc                                                                                                                     <  2:632859/139‑1 (MQ=255)

       aCCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGc                                                                                                                     <  1:121686/139‑1 (MQ=255)

               aaCGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAg                                                                                                             >  1:699770/1‑139 (MQ=255)

               aaCGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAg                                                                                                             >  2:119116/1‑139 (MQ=255)

               aaCGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAg                                                                                                             >  1:526729/1‑139 (MQ=255)

               aaCGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAg                                                                                                             <  2:452296/139‑1 (MQ=255)

                            cTATCTTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGTCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATATTTACGGCCTTTCCAGGTGTAGTCACCcg                                                                                                <  1:443747/139‑1 (MQ=255)

                            cTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCcg                                                                                                >  1:314914/1‑139 (MQ=255)

                            cTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCcg                                                                                                <  1:164098/139‑1 (MQ=255)

                                     tgtTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACa                                                                                        >  1:99583/1‑139 (MQ=255)

                                     tgtTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTc                                                                                                                >  2:134367/1‑114 (MQ=255)

                                     tgtTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTc                                                                                                                <  1:134367/114‑1 (MQ=255)

                                         ccAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAg                                                                                   >  1:602038/1‑139 (MQ=255)

                                              aaaTTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTAt                                                                              <  2:602038/139‑1 (MQ=255)

                                               aaTTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATc                                                                             <  2:271745/139‑1 (MQ=255)

                                                 ttGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGa                                                                           <  1:119116/139‑1 (MQ=255)

                                                    aGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGc                                                                        <  1:68133/139‑1 (MQ=255)

                                                      cgtcgtCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTg                                                                      >  1:584307/1‑139 (MQ=255)

                                                            cAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGatatat                                                                <  2:314914/139‑1 (MQ=255)

                                                                                 aTCATTCCACGGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCgcagc                                            <  2:99583/139‑1 (MQ=255)

                                                                                     ttCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGaa                                       >  1:377007/1‑139 (MQ=255)

                                                                                             gTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGt                                >  2:111264/1‑139 (MQ=255)

                                                                                              tttAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTa                               >  1:588830/1‑139 (MQ=255)

                                                                                                 aGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCg                            >  1:339548/1‑139 (MQ=255)

                                                                                                   gCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGaa                          <  1:345162/139‑1 (MQ=255)

                                                                                                        tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAatga                     <  2:377007/139‑1 (MQ=255)

                                                                                                           aTAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATgg                  <  2:339548/139‑1 (MQ=255)

                                                                                                                 aCGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTc            <  2:584307/139‑1 (MQ=255)

                                                                                                                      gCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTc       >  1:249673/1‑139 (MQ=255)

                                                                                                                           tcccgtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGc  <  1:111264/139‑1 (MQ=255)

CGCCTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCAC‑GGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTACCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGC  >  NC_000913/1595297‑1595557

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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