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	1,203,224	G→A	67 (TAG→TAA)	croE →	e14 prophage, putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,203,224	0	G	A	100.0%	102.7 / NA	32	67 (TAG→TAA)	croE	e14 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (17/15); total (17/15)

AATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAGCAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAGTGGTTAC  >  NC_000913/1203117‑1203357

aaTGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACg                                                                                                        <  1:128881/139‑1 (MQ=255)

       ataAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGc                                                                                                 <  2:64791/139‑1 (MQ=255)

              aGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGc                                                                                                 <  1:1068039/132‑1 (MQ=255)

              aGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGc                                                                                                 >  2:1068039/1‑132 (MQ=255)

                   gTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTa                                                                                     >  1:217313/1‑139 (MQ=255)

                    ttttGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTaa                                                                                    >  2:618409/1‑139 (MQ=255)

                                              aaTACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGc                                                          <  1:265206/139‑1 (MQ=255)

                                                 acacATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTg                                                       >  2:843340/1‑139 (MQ=255)

                                                   acaTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAg                                                     <  1:897823/139‑1 (MQ=255)

                                                   acaTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAg                                                     <  1:143636/139‑1 (MQ=255)

                                                     aTCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTg                                                   <  2:217313/139‑1 (MQ=255)

                                                      tCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTgg                                                  <  1:618409/139‑1 (MQ=255)

                                                       cAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGAGGt                                                 >  2:273192/1‑139 (MQ=255)

                                                          gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGt                                                                                          >  1:1096107/1‑95 (MQ=255)

                                                          gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGt                                                                                          <  2:1096107/95‑1 (MQ=255)

                                                          gTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACg                                              >  1:593854/1‑139 (MQ=255)

                                                            gCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGaaa                                                                <  1:1024074/119‑1 (MQ=255)

                                                            gCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGaaa                                                                >  2:1024074/1‑119 (MQ=255)

                                                               aTTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGAt                                                                                                      >  1:576879/1‑78 (MQ=255)

                                                               aTTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGAt                                                                                                      <  2:576879/78‑1 (MQ=255)

                                                               aTTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATc                                                                                            >  1:446030/1‑88 (MQ=255)

                                                               aTTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATc                                                                                            <  2:446030/88‑1 (MQ=255)

                                                                       aTCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAg                                 <  1:550021/139‑1 (MQ=255)

                                                                        tCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGa                                >  2:190831/1‑139 (MQ=255)

                                                                        tCTGACTTAAGACCGGATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGa                                >  1:163153/1‑139 (MQ=255)

                                                                                      ggATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCgcggc                  >  2:1125607/1‑139 (MQ=255)

                                                                                       gATATCTATCCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCgcggcg                 >  2:169244/1‑139 (MQ=255)

                                                                                              atcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATcg                      <  2:1125489/127‑1 (MQ=255)

                                                                                              atcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATcg                      >  1:1125489/1‑127 (MQ=255)

                                                                                               tcCGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAg         >  2:569832/1‑139 (MQ=255)

                                                                                                 cGAAAGATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAGTg       >  2:412468/1‑139 (MQ=255)

                                                                                                      gATTAACAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAGTGGTTAc  <  1:843340/139‑1 (MQ=255)

AATGGCTATAAAAAAGCCAGTTTTGTGCTGGCTAAAAAACTTGAGCAATACACATCAGGTGCAATTACGAAATCTGACTTAAGACCGGATATCTATCCGAAAGATTAGCAGAACACTTTCAATTTTTAACCACAGAACGATGAGGCTAATCGTGGGTAAGCATCACTGGAAAATAGAAAAACAGCCTGAGTGGTACGTGAAAGCTGTCAGAAAAACTATCGCGGCGTTGCCGAGTGGTTAC  >  NC_000913/1203117‑1203357

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