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 F11 I1 R1	56	91.5	3907174	98.4%	3844659	146.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947_CJ‑RC	4,741,338	C→G	intergenic (+468/+285)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	4,741,338	0	C	G	94.7%	128.4 / 0.2	38	intergenic (+468/+285)	gltA/yeiW	citrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand): ref base C (0/2); new base G (15/21); total (15/23)
Fisher's exact test for biased strand distribution p-value = 5.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

TCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAACCAAGCAAAAGGCCCCGAAAAGGCCCT‑CC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCA  >  NC_002947_CJ‑RC/4741229‑4741470

tCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGcccc                                                                                                 >  8:450429/1‑149 (MQ=255)

  cGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGcccc                                                                                                 >  5:171966/1‑147 (MQ=255)

   gCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCgga                                                                                              >  7:384032/1‑147 (MQ=255)

    cctcctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCCGCGACTTGC‑ATTCGTGAATCCAGGCACAGGCCCCgga                                                                                              <  6:428993/148‑3 (MQ=255)

      tcctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGCTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTCCATTCGTGAATCCAGGCACAGGCCCCggacac                                                                                           >  7:142318/1‑144 (MQ=255)

               gTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGtcct‑cct                                                                                  <  1:325291/148‑2 (MQ=255)

                        tgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGcgcctc                                                                        <  7:168852/149‑3 (MQ=255)

                          cagcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGcgcctcga                                                                      >  2:270179/1‑145 (MQ=255)

                           agcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGcgcctcgac                                                                     <  3:440692/149‑6 (MQ=255)

                             caCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGcgcctcgacct                                                                   >  4:67797/1‑142 (MQ=255)

                                    tCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAg                                                            >  2:33453/1‑149 (MQ=255)

                                        gcggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAgcggc                                                        <  4:214869/149‑1 (MQ=255)

                                           gcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGgggc                                                      <  6:204154/148‑1 (MQ=255)

                                            cttCACCTGCCTTGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTGGTTCTTGAGCAGCTTCTGCGAGTTGC‑ATTCGTTAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCTGCGCCt                                                    <  7:221261/147‑1 (MQ=255)

                                             gTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCtt                                                   <  3:465590/149‑1 (MQ=255)

                                                 ccGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGAt                                                >  8:292406/1‑148 (MQ=255)

                                                  cGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGTTCa                                              <  4:377795/149‑1 (MQ=255)

                                                  cGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATc                                               >  5:86437/1‑148 (MQ=255)

                                                    gCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACg                                            <  7:417882/149‑1 (MQ=255)

                                                    gCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACg                                            <  1:270179/149‑1 (MQ=255)

                                                     ccATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACgg                                           <  8:955/149‑1 (MQ=255)

                                                       aTGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTc                                         <  8:406660/149‑1 (MQ=255)

                                                        tGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACCCGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCATGATCACGGTc                                         >  5:13793/1‑148 (MQ=255)

                                                            gTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACAcc                                    <  1:261970/149‑1 (MQ=255)

                                                                 gAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGa                                <  7:117825/148‑1 (MQ=255)

                                                                   aCTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATa                              <  5:453350/148‑1 (MQ=255)

                                                                       ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGc                           <  1:216251/147‑1 (MQ=255)

                                                                       ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGc                           <  2:351932/147‑1 (MQ=255)

                                                                        gTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGcc                          <  6:350757/147‑1 (MQ=255)

                                                                         tttaGGTCCAGCTCTGGTCACCTTCGTGCTTGTG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCTGCT‑GCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTg                       <  2:414878/147‑1 (MQ=255)

                                                                           taGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTa                     <  2:295198/149‑1 (MQ=255)

                                                                              gTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                  >  8:259210/1‑149 (MQ=255)

                                                                              gTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                  >  2:272411/1‑149 (MQ=255)

                                                                                ccAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTg                 <  5:388880/148‑1 (MQ=255)

                                                                                  aGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAc              <  1:13353/149‑1 (MQ=255)

                                                                                    ctctGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAcc             >  6:208803/1‑148 (MQ=255)

                                                                                              cTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCa  >  2:140002/1‑149 (MQ=255)

                                                                                              cTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAGGCCCCGGACACGTCCT‑CCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCa  >  8:491009/1‑149 (MQ=255)

TCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAACCAAGCAAAAGGCCCCGAAAAGGCCCT‑CC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCA  >  NC_002947_CJ‑RC/4741229‑4741470

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A