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
A1 F1 I2 R1	765	46.1	2269152	93.8%	2128464	105.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,381,789	G→A	pseudogene (13/126 nt)	ycjV →	pseudogene, putative ATP‑binding component of a transport system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,381,789	0	G	A	100.0%	108.5 / NA	34	pseudogene (13/126 nt)	ycjV	pseudogene, putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (17/17); total (17/17)

ATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAGTGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCATTC  >  NC_000913/1381661‑1381921

aTGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGc                                                                                                                            >  2:594305/1‑139 (MQ=255)

    gAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGt                                                                                                                        <  2:1045737/139‑1 (MQ=255)

    gAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGt                                                                                                                        <  1:1111852/139‑1 (MQ=255)

         cGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGt                                                                                                                                  >  2:1076338/1‑124 (MQ=255)

         cGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGt                                                                                                                                  <  1:1076338/124‑1 (MQ=255)

             cGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAATCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAAt                                                                                                               <  1:1018767/139‑1 (MQ=255)

                            cGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGga                                                                                                <  2:567381/139‑1 (MQ=255)

                              gACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGgaga                                                                                              >  1:897222/1‑139 (MQ=255)

                                   gcAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAata                                                                                         >  1:466691/1‑139 (MQ=255)

                                         ggAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTa                                                                                   <  2:441949/139‑1 (MQ=255)

                                                  cATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTa                                                                                   <  1:1049192/130‑1 (MQ=255)

                                                  cATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTa                                                                                   >  2:1049192/1‑130 (MQ=255)

                                                                        gCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTg                                                                                                                          >  1:580751/1‑69 (MQ=255)

                                                                        gCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTg                                                                                                                          <  2:580751/69‑1 (MQ=255)

                                                                        gCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCtt                                                    >  1:487731/1‑139 (MQ=255)

                                                                                 aCCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGa                                           >  1:101561/1‑139 (MQ=255)

                                                                                      tGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAAt                                                                                                               >  2:906374/1‑66 (MQ=255)

                                                                                      tGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAAt                                                                                                               <  1:906374/66‑1 (MQ=255)

                                                                                                aTGCTCTACACCACTGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGTAAt                            <  1:772599/139‑1 (MQ=255)

                                                                                                  gCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAAt                            >  1:504800/1‑137 (MQ=255)

                                                                                                  gCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAAt                            <  2:504800/137‑1 (MQ=255)

                                                                                                     ctACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAg                                                                                                  >  1:883843/1‑64 (MQ=255)

                                                                                                     ctACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAg                                                                                                  <  2:883843/64‑1 (MQ=255)

                                                                                                      tACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTa                      <  2:487731/139‑1 (MQ=255)

                                                                                                       acacCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTaa                     <  2:897222/139‑1 (MQ=255)

                                                                                                             cGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGga                                                                                                <  1:885880/58‑1 (MQ=255)

                                                                                                             cGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGga                                                                                                >  2:885880/1‑58 (MQ=255)

                                                                                                             cGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATc                                                                                       >  1:872176/1‑67 (MQ=255)

                                                                                                             cGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATc                                                                                       <  2:872176/67‑1 (MQ=255)

                                                                                                             cGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAg               >  1:604577/1‑139 (MQ=255)

                                                                                                                ttGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACgg                                      >  1:787431/1‑113 (MQ=255)

                                                                                                                ttGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACgg                                      <  2:787431/113‑1 (MQ=255)

                                                                                                                  gggggCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGa          >  1:746147/1‑139 (MQ=255)

                                                                                                                     ggCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAgg       >  2:988866/1‑139 (MQ=255)

                                                                                                                          gAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCATTc  >  2:485008/1‑139 (MQ=255)

ATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAGTGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCATTC  >  NC_000913/1381661‑1381921

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