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
A23 F107 I0 R1	44	28.8	1140136	90.5%	1031823	142.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,184,543	C→A	100%	P1100Q (CCG→CAG)	rpoB →	RNA polymerase subunit beta

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,543	0	C	A	100.0%	112.9 / NA	36	P1100Q (CCG→CAG)	rpoB	RNA polymerase subunit beta
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (22/14); total (22/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCAGC  >  NC_000913/4184405‑4184683

tGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAAGTGCTAAGATGAACCCGATCGAAGATATGCCTTACGATGGAAACGGTACGCCGGTGGACATCGTACTCAACCAGCTg                                                                                                                                          >  2:217155/1‑143 (MQ=255)

  gCGGTTAAGCGCCGTAACCAGGCTGATGACAAGAGGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGAGCAACCCGAGCGAAGATATGCCTTACGATGAAAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTggg                                                                                                                                        <  2:62250/143‑1 (MQ=255)

          aCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGt                                                                                                                                >  1:482578/1‑143 (MQ=255)

                 aTCCAGCCCGGTGACATGATTGCAGGTCGTCACGGTAACAAGAGTGTGATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAt                                                                                                                         <  2:338274/143‑1 (MQ=255)

                   ccAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGa                                                                                                                       <  1:50310/143‑1 (MQ=255)

                    cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGGTCAACACGGACGAAGCTATGCCTTACGATGAAACCGGTACGCCGGTAGACAGCGTCCTGAACCAGCTTCGCGGCCCGACTCGTATGaa                                                                                                                      >  1:182183/1‑143 (MQ=255)

                    cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGAGCGAAGGTATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGACCCAGCTGGGGGTGCCGTCTCGGGTGaa                                                                                                                      >  1:182177/1‑143 (MQ=255)

                     aGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGagc                                                                                                                     >  1:145426/1‑141 (MQ=255)

                             gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                             <  2:482578/143‑1 (MQ=255)

                             gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                             <  2:563013/143‑1 (MQ=255)

                                 aGATGGCAGGGCGACACGGTAACAAGGGTGTAATTTCGGAGGTCAACCCCATCGACGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATc                                                                                                         <  1:269738/143‑1 (MQ=255)

                                    tGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTc                                                                                                      <  2:511772/143‑1 (MQ=255)

                                    tGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTc                                                                                                      <  2:514252/143‑1 (MQ=255)

                                    tGGCAGGTCGTCACGGTAACAAGGGCGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTc                                                                                                      <  1:86470/143‑1 (MQ=255)

                                          gtcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAGCATCGGTCAGATCCTCGAAAcc                                                                                                >  2:477715/1‑143 (MQ=255)

                                                aCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGCTCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGGCTCGCATGAACATAGGCCAGATCCCAGAACCCCAccgc                                                                                          >  2:313749/1‑141 (MQ=255)

                                                  ggTAACAAGGGTGTAAGTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTggg                                                                                        <  1:354122/143‑1 (MQ=255)

                                                    tAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGtg                                                                                      >  1:85226/1‑142 (MQ=255)

                                                          gggTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACCTCGGTCAGATCCTCGAGACCCACCGGGGGATGGCTg                                                                                >  1:191027/1‑143 (MQ=255)

                                                                aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                          <  2:12521/143‑1 (MQ=255)

                                                                    tCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGCACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGCAAGGTAt                                                                      >  2:110074/1‑143 (MQ=255)

                                                                      tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCACATCCTCGAAACCCACCCGGGTATGGCAGCGAAAGGTacag                                                                    >  2:497101/1‑140 (MQ=255)

                                                                            cAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCCGCGAcc                                                              >  2:372502/1‑142 (MQ=255)

                                                                               cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTCCTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCCGGGAATGGACCGGAAAGGTATCGGCCGCAAgg                                                           >  2:137802/1‑142 (MQ=255)

                                                                               cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTAGTATGAACATCGCTCAGATCCCCGAAACCCAGCCGGGTATGGCTGCGAAAGGTATCGGCGGCAAGa                                                           >  2:252472/1‑143 (MQ=255)

                                                                                 cGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGGTc                                                         <  1:328427/143‑1 (MQ=255)

                                                                                  gATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACCAGATCa                                                        >  1:308320/1‑143 (MQ=255)

                                                                                   aTCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATACCCGAAACCCACCTGGGTATGGCTGCGCAAGGTATCGGCGCCAAGATCaa                                                       >  1:340312/1‑143 (MQ=255)

                                                                                          atatGCCTTGCGCTGACAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACACCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATg                                                <  2:540580/143‑1 (MQ=255)

                                                                                          atatGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTAGCGGCGACAAGATCAACGCCATg                                                >  2:555290/1‑143 (MQ=255)

                                                                                                      aTGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTCTGAACATCGGTCAGATCCTCGAAACCCACCTGGGTCTGGCTGCGAACGGCATCGGCGACAAGCGCCACGCCCTCCTCACAcagcag                                    >  1:20943/1‑143 (MQ=255)

                                                                                                            aCGGTACGCCGGTAGACATCGTACTGAACGAGCTGGGCGTACCGTCTCGTATGAACATCGGTCGGATGCTAGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAGCAGAAGCaagag                              >  1:22458/1‑142 (MQ=255)

                                                                                                                  cGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGGTGAAACAGAAGCAAGAAGAcgcg                        >  2:104083/1‑143 (MQ=255)

                                                                                                                   gCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGa                       >  2:172370/1‑143 (MQ=255)

                                                                                                                                    tGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATc      >  2:457370/1‑143 (MQ=255)

                                                                                                                                    ggAACCAGCTGGGCGTCCCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCATCTGGGTATGGCTGAGAAAGGTATCGGCGACAAGATCAACGCCATGATGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATc      <  2:96934/142‑1 (MQ=255)

                                                                                                                                        cccGCTCGGCGTACCATCTCGTATGACCATCGGTCAGATACTCGAACCAAAACTGCGTATGGCTGCGAAAGGTACCGGCGACAAGATCAACGCCATGCTAAATCACCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCAgc  <  2:145426/143‑1 (MQ=255)

TGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCAGC  >  NC_000913/4184405‑4184683

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A