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
A5 F1 I2 R1	772	77.0	3769570	91.6%	3452926	105.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,994,415	G→A	pseudogene (34/60 nt)	pbl →	pseudogene, peptidoglycan‑binding enzyme family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,994,415	0	G	A	98.2%	179.1 / NA	56	pseudogene (34/60 nt)	pbl	pseudogene, peptidoglycan‑binding enzyme family
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (29/26); minor base C (1/0); total (30/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTC  >  NC_000913/2994287‑2994545

ttttCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTaa                                                                                                                          >  2:364922/1‑139 (MQ=255)

      cGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTc                                                                                                                    >  1:1554774/1‑139 (MQ=255)

        ttGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAg                                                                                                                  <  1:1480838/139‑1 (MQ=255)

          gtgGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCa                                                                                                                >  1:1634248/1‑139 (MQ=255)

          gtgGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCa                                                                                                                >  1:1458473/1‑139 (MQ=255)

                     tGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGt                                                                                                                            <  2:830760/116‑1 (MQ=255)

                     tGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATAGt                                                                                                                            >  1:830760/1‑116 (MQ=255)

                                  ggACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCtttttt                                                                                        >  1:1607275/1‑139 (MQ=255)

                                       tataATGCGGGTTTTTCAATGGATAACCCAAAAAAGAGACAGCAATATGCCCCAAAATATATCTGGTATATAACAGGCTTAATGAATTACATAATCGTAACTCTTCAGCACAATGAGCCTAAAGCCTCTTTTTTCtata                                                                                   >  1:1391102/1‑139 (MQ=255)

                                       tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtata                                                                                   <  1:364922/139‑1 (MQ=255)

                                       tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtat                                                                                    >  1:677948/1‑138 (MQ=255)

                                       tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtat                                                                                    <  2:677948/138‑1 (MQ=255)

                                             gCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCGCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCATAATGAGAATAAAGCCTCATTTTTTtataaattac                                                                             >  1:443359/1‑133 (MQ=255)

                                              cGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGTAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  2:1242968/122‑1 (MQ=255)

                                              cGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtatat                                                                                  <  2:202252/133‑1 (MQ=255)

                                              cGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtatat                                                                                  >  1:202252/1‑133 (MQ=255)

                                              cGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCa                                                                            <  1:1621099/139‑1 (MQ=255)

                                              cGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATAGTGAATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  1:1242968/1‑122 (MQ=255)

                                                ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                          >  2:223149/1‑139 (MQ=255)

                                                ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                          <  1:223149/139‑1 (MQ=255)

                                                     tGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACAccc                                                                     <  2:1554774/139‑1 (MQ=255)

                                                                  cAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTg                                                        <  1:338879/139‑1 (MQ=255)

                                                                         agagACAGCAATATGCCCCGAAATATATATGGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGAt                                                 <  2:1391102/139‑1 (MQ=255)

                                                                                    tatGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATAc                                      <  2:1607275/139‑1 (MQ=255)

                                                                                         cccAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       >  2:1159909/1‑133 (MQ=255)

                                                                                         cccAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       <  1:1159909/133‑1 (MQ=255)

                                                                                            aaaaTATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGa                              <  2:1634248/139‑1 (MQ=255)

                                                                                                       tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtat                                                                                    >  2:423364/1‑74 (MQ=255)

                                                                                                       tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtat                                                                                    <  1:423364/74‑1 (MQ=255)

                                                                                                        gTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACAt                          >  1:767187/1‑131 (MQ=255)

                                                                                                        gTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACAt                          <  2:767187/131‑1 (MQ=255)

                                                                                                        gTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttc                  >  1:57060/1‑139 (MQ=255)

                                                                                                         tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAttt                   <  2:1129784/137‑1 (MQ=255)

                                                                                                         tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAttt                   >  1:1129784/1‑137 (MQ=255)

                                                                                                         tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                 <  2:57060/139‑1 (MQ=255)

                                                                                                           tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGCTTTGATCAACTCGATACCACTGTGAACATCTAATttcttc               >  2:165086/1‑139 (MQ=255)

                                                                                                              aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCaa                                              <  2:991951/105‑1 (MQ=255)

                                                                                                              aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCaa                                              >  1:991951/1‑105 (MQ=255)

                                                                                                              aCCAGGCTTAATGAACTAAACAATCGTAAGGCCTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATg            >  2:159639/1‑139 (MQ=255)

                                                                                                                 aGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGata         >  1:702236/1‑139 (MQ=255)

                                                                                                                   gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  1:553012/53‑1 (MQ=255)

                                                                                                                   gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  2:553012/1‑53 (MQ=255)

                                                                                                                   gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  1:292006/53‑1 (MQ=255)

                                                                                                                   gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  2:292006/1‑53 (MQ=255)

                                                                                                                   gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                          <  1:1621677/72‑1 (MQ=255)

                                                                                                                   gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                          >  2:1621677/1‑72 (MQ=255)

                                                                                                                   gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAttt                   <  2:1854447/127‑1 (MQ=255)

                                                                                                                   gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAttt                   >  1:1854447/1‑127 (MQ=255)

                                                                                                                   gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt       >  1:1398758/1‑139 (MQ=255)

                                                                                                                   gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt       >  2:986553/1‑139 (MQ=255)

                                                                                                                      tAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAg    <  2:1398758/139‑1 (MQ=255)

                                                                                                                        aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  1:1390102/48‑1 (MQ=255)

                                                                                                                        aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  2:1390102/1‑48 (MQ=255)

                                                                                                                        aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                 <  1:134326/124‑1 (MQ=255)

                                                                                                                        aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                 >  2:134326/1‑124 (MQ=255)

                                                                                                                        aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTc  >  1:1461327/1‑139 (MQ=255)

TTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTC  >  NC_000913/2994287‑2994545

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A