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
A10 F64 I0 R1	409	63.1	2344228	95.5%	2238737	135.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,177,586	T→C	88.9%	L770P (CTC→CCC)	rpoC →	RNA polymerase, beta prime subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,177,586	0	T	C	88.9%	137.2 / 7.9	45	L770P (CTC→CCC)	rpoC	RNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand): ref base T (3/2); new base C (28/12); total (31/14)
Fisher's exact test for biased strand distribution p-value = 6.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCCGACTCCGGTGCGCGTGGTTCTGCGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACTCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTGGTTGACGTGGCGCAGGACCTGGTGGTTACCGAAG  >  CP009273/4177452‑4177711

ggCCGACTCCGGTGCGCGTGGTTCTGCGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGt                                                                                                                          >  1:236232/1‑140 (MQ=255)

    gACTCCGGTGCGCGTGGTTCTGCGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACtt                                                                                                                      >  2:215085/1‑140 (MQ=255)

    gACTCCGGTGCGCGTGGTTCTGCGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACtt                                                                                                                      >  2:800590/1‑140 (MQ=255)

          ggTGCGCGTGGTTCTGCGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCAtctc                                                                                                                <  1:47564/140‑1 (MQ=255)

                 gTGGTTCTGCGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTccacccac                                                                                                         >  1:464039/1‑140 (MQ=255)

                    gTTCTGCGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGt                                                                                                      <  2:587611/140‑1 (MQ=255)

                        tGCGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTc                                                                                                  >  2:467338/1‑140 (MQ=255)

                          cGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGt                                                                                                >  1:743762/1‑140 (MQ=255)

                          cGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGt                                                                                                >  1:294502/1‑140 (MQ=255)

                          cGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGt                                                                                                >  1:372383/1‑140 (MQ=255)

                             cacaGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTaaa                                                                                             >  2:1025556/1‑140 (MQ=255)

                               caGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAgg                                                                                           >  1:990070/1‑140 (MQ=255)

                               caGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAgg                                                                                           >  1:726877/1‑140 (MQ=255)

                                aGATTCGTCAGCTTGCTTGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCAATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGt                                                                                          <  1:607904/140‑1 (MQ=255)

                                aGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGt                                                                                          <  2:306086/140‑1 (MQ=255)

                                aGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGt                                                                                          <  1:65058/140‑1 (MQ=255)

                                aGATTCGTCAGCTTGCTGGTATGCGTGGTCCGATGGCGAAGCCGGATGGCTCCATCATCGAAACCCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGt                                                                                          <  1:526368/140‑1 (MQ=255)

                                  aTTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCt                                                                                        >  2:76201/1‑140 (MQ=255)

                                  aTTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCt                                                                                        >  2:43996/1‑140 (MQ=255)

                                          gCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAACCGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACTCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATa                                                                                >  2:621970/1‑140 (MQ=255)

                                                       cGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAAc                                                                   >  2:197156/1‑140 (MQ=255)

                                                       cGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAAc                                                                   >  2:780248/1‑140 (MQ=255)

                                                       cGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAAc                                                                   >  2:433266/1‑140 (MQ=255)

                                                       cGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAAc                                                                   >  2:288600/1‑140 (MQ=255)

                                                       cGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAAc                                                                   >  2:409952/1‑140 (MQ=255)

                                                       cGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAAc                                                                   >  2:419721/1‑140 (MQ=255)

                                                            tCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGc                                                                            <  1:19720/126‑1 (MQ=255)

                                                            tCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGc                                                                            >  2:19720/1‑126 (MQ=255)

                                                                      aaGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGACGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGttc                                                    >  1:922953/1‑139 (MQ=255)

                                                                      aaGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTa                                                    >  1:923138/1‑140 (MQ=255)

                                                                      aaGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTa                                                    >  1:425155/1‑140 (MQ=255)

                                                                      aaGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTa                                                    >  1:270126/1‑140 (MQ=255)

                                                                      aaGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGGAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTa                                                    >  1:779527/1‑140 (MQ=255)

                                                                      aaGCCGGATGGCTCCATCATCGAAACGCAAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCAATGAAAACTGCGAACTCCGGTTa                                                    >  1:361319/1‑140 (MQ=255)

                                                                                      tcatcGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACTCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTg                                    >  1:230526/1‑140 (MQ=255)

                                                                                      tcatcGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACTCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTg                                    >  1:461071/1‑140 (MQ=255)

                                                                                             aaCGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTGGTTGACg                             <  1:972521/140‑1 (MQ=255)

                                                                                             aaCGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTGGTTGACg                             <  1:518223/140‑1 (MQ=255)

                                                                                             aaCGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTGGTTGACg                             <  1:33326/140‑1 (MQ=255)

                                                                                                    aTCACCGCGAACTTCCGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTGGTTGACGTGGCGCa                      <  2:236232/140‑1 (MQ=255)

                                                                                                    aTCACCGCGAACGTCCGTGAAGGTCTGAACGTACTCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGACCTCCGGTTACCTGACTCGTCGTCTGGTTGACGTGGCGCa                      <  2:490596/140‑1 (MQ=255)

                                                                                                                   cGTGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTGGTTGACGTGGCGCAGGACCTGGTGGTTAc       >  1:989522/1‑140 (MQ=255)

                                                                                                                    gTGAAGGTCTGAACGTACTCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTGGTTGACGTGGCGCAGGACCTGGTGGTTAcc      <  2:230526/140‑1 (MQ=255)

                                                                                                                     tGAAGGTCTGAACGTACCCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTGGTTGACGTGGCGCAGGACCTGGTGGTTACCg     >  2:1126558/1‑140 (MQ=255)

                                                                                                                        aGGTCTGAACGTACCCCAGTACTTCATCTCCACACACGGTTCAAGTAAACGTCTGGCGGATACAGCAATGAAAACTGAGAACTCCTGTTACCTTACTCGTCGTCTGGTTGACGTGGCGCAGTACCTGGTGGTTACCGAAg  <  2:914614/140‑1 (MQ=255)

GGCCGACTCCGGTGCGCGTGGTTCTGCGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCTGAACGTACTCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTGGTTGACGTGGCGCAGGACCTGGTGGTTACCGAAG  >  CP009273/4177452‑4177711

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 11 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A