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	2,765,829	(C)_5→4	intergenic (‑53/‑89)	yfjM ← / → rnlA	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,765,825	0	C	.	100.0%	200.9 / NA	50	intergenic (‑49/‑93)	yfjM/rnlA	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (25/25); total (25/25)

GGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGT  >  NC_000913/2765697‑2765952

ggCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAg                                                                                                                      <  2:1328424/139‑1 (MQ=255)

      taatTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCt                                                                                                                <  1:299252/139‑1 (MQ=255)

              aaGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                        <  1:1724610/139‑1 (MQ=255)

                 tATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCaa                                                                                                     >  2:1467068/1‑139 (MQ=255)

                      aGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCaa                                                                                                >  1:137392/1‑139 (MQ=255)

                           ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGCGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATacac                                                                                           >  2:1749616/1‑139 (MQ=255)

                                      gaTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGt                                                                                >  1:1502502/1‑139 (MQ=255)

                                       aTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                               <  2:137392/139‑1 (MQ=255)

                                            gAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                   >  1:1239223/1‑114 (MQ=255)

                                            gAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                   <  2:1239223/114‑1 (MQ=255)

                                               gagGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTa                                                                       <  1:1467068/139‑1 (MQ=255)

                                                agGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTag                                                                      >  2:208394/1‑139 (MQ=255)

                                                 ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTaga                                                                     >  1:539552/1‑139 (MQ=255)

                                                  gTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTagag                                                                    >  1:931768/1‑139 (MQ=255)

                                                  gTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTagag                                                                    >  2:512008/1‑139 (MQ=255)

                                                  gTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTagag                                                                    >  1:1465648/1‑139 (MQ=255)

                                                                      catcCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg                                                <  2:1502502/139‑1 (MQ=255)

                                                                       atcCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATgg                                               >  2:708152/1‑139 (MQ=255)

                                                                           cccATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATc                                           <  2:539552/139‑1 (MQ=255)

                                                                           cccATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATc                                           <  1:708152/139‑1 (MQ=255)

                                                                                tttGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                      <  2:124852/91‑1 (MQ=255)

                                                                                tttGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                      >  1:124852/1‑91 (MQ=255)

                                                                                    tgGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATg                                  <  1:512008/139‑1 (MQ=255)

                                                                                         tGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                      >  2:822396/1‑82 (MQ=255)

                                                                                         tGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                      <  1:822396/82‑1 (MQ=255)

                                                                                           cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                   >  2:253564/1‑67 (MQ=255)

                                                                                           cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                   <  1:253564/67‑1 (MQ=255)

                                                                                           cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATTCACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGaaa                                    <  1:238644/130‑1 (MQ=255)

                                                                                           cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCa                                                                                       >  1:175022/1‑79 (MQ=255)

                                                                                           cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCa                                                                                       <  2:175022/79‑1 (MQ=255)

                                                                                           cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                               <  2:1097051/87‑1 (MQ=255)

                                                                                           cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                               >  1:1097051/1‑87 (MQ=255)

                                                                                           cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGaaa                                    >  2:238644/1‑130 (MQ=255)

                                                                                           cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCa                           >  2:227921/1‑139 (MQ=255)

                                                                                                     aGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACaa                 <  1:227921/139‑1 (MQ=255)

                                                                                                       aCGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                      >  2:1414953/1‑68 (MQ=255)

                                                                                                       aCGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                      <  1:1414953/68‑1 (MQ=255)

                                                                                                           tCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                              <  2:922895/56‑1 (MQ=255)

                                                                                                           tCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                              >  1:922895/1‑56 (MQ=255)

                                                                                                            ccTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTa          >  2:1009641/1‑139 (MQ=255)

                                                                                                             ctgtccTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATc                            >  2:218240/5‑120 (MQ=255)

                                                                                                             ctgtccTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATc                            <  1:218240/116‑1 (MQ=255)

                                                                                                              tGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTaaa        >  1:604760/1‑139 (MQ=255)

                                                                                                               gCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAAt       <  2:604760/139‑1 (MQ=255)

                                                                                                                cccTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACCTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATc      >  1:343166/1‑139 (MQ=255)

                                                                                                                   tataGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTT‑AATCTGGt  <  1:1009641/139‑1 (MQ=255)

                                                                                                                    ataGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTACATCTGGt  <  1:208394/139‑1 (MQ=255)

                                                                                                                    ataGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGt  <  1:1749616/139‑1 (MQ=255)

                                                                                                                          ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACt            >  2:1544991/1‑123 (MQ=255)

                                                                                                                          ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACt            <  1:1544991/123‑1 (MQ=255)

GGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGT  >  NC_000913/2765697‑2765952

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