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
A4 F13 I0 R1	140	52.5	2164708	98.8%	2138731	146.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947_CJ‑RC	3,447,291	T→G	22.6%	A19A (GCT→GCG)	PP_5556 →	bacteriophage lysis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	3,447,291	0	T	G	22.6%	59.1 / 3.0	38	A19A (GCT→GCG)	PP_5556	bacteriophage lysis protein
Reads supporting (aligned to +/- strand): ref base T (24/3); new base G (2/7); total (28/10)
Fisher's exact test for biased strand distribution p-value = 4.27e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCT  >  NC_002947_CJ‑RC/3447146‑3447434

aTCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTg                                                                                                                                                <  7:240741/147‑1 (MQ=255)

   cTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTggcg                                                                                                                                             >  5:177402/1‑147 (MQ=255)

                  cGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCt                                                                                                                              >  5:188516/1‑147 (MQ=255)

                             tggtAGCAAGGGTCGGGAGGTCCTCAAGGCCCTATACACGCGAGCGCGCGTGGTGCTGCAGTGAGGGCTTGGGCCACCCGCCTGGGCGCGGTGGGGGTGCTGCTGGCCGCCTGCGGGGGCGGCGCCCGGGCAGCCTGGGTGTGGCa                                                                                                                    <  2:30110/146‑1 (MQ=255)

                              ggtAGCATCGGTCTGGAGGATCGCAAGGCCCTCTACATGCGCGCGCTCGAGGTGCTGCTGTGAGGGCTTGGGCCACCCGCGTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAgg                                                                                                                  <  8:164123/147‑1 (MQ=255)

                                   cAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAAc                                                                                                             >  8:170380/1‑147 (MQ=255)

                                      cGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGc                                                                                                                                   >  7:115367/1‑122 (MQ=255)

                                               ggaTCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCAGGCGGCGCCCCGGCAGCCGGGGTGTGGCAGGCCAACCCCGAAAAcgcg                                                                                                 >  8:99630/1‑147 (MQ=255)

                                                gaTCGCAAGGCCCTCTACAAGTGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCCGCCTGGGTGTGGCAGGCCACCGCCTATAAGgc                                                                                                  >  7:240383/1‑145 (MQ=255)

                                                   cGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCGGGCGGCGCCCGGGCAGCCGGGGTGTGGCAGGCCAACGCCGATAAGGCGCAGc                                                                                             >  5:177961/1‑147 (MQ=255)

                                                       aGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGc                                                                                         >  5:238432/1‑147 (MQ=255)

                                                         gCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCGGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTg                                                                                       >  6:107854/1‑147 (MQ=255)

                                                           ccTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCGGGGTGGGGCTGGGCCACGCCAAAAATGCGCACCTCGCTGa                                                                                      >  3:41476/1‑146 (MQ=255)

                                                            ctctACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCCGGCAGCCAGCGTGTTGCAGGCCAACCCCTAAAAACCGCACCTCGCTGaa                                                                                     >  7:95545/1‑145 (MQ=255)

                                                             tctACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCa                                                                                   >  6:139238/1‑147 (MQ=255)

                                                               aacacGCGCGCGCTCGGGGGGCGGCTGGGCGCGGTGGGCCCCCCCGCGGGGGCGCGGGGGCGCTGCTGCGGGCCGCCAGGGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAgg                                                                                 <  7:210259/146‑1 (MQ=255)

                                                                 cAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCGGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGc                                                                                >  1:2443/1‑146 (MQ=255)

                                                                 cAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCCGGCAGCCTGGGGGTGGCAGGCCCACCCCGATAATGCGCAGCGCGCAGATCAGGcc                                                                               >  4:172072/1‑147 (MQ=255)

                                                                     cgagcgCTCGAGGTGCTGCAGTGAGCGCTTGGGCAACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCCCCCGCGCAGGCGGCGCCCCGGCAGCCTGGGAGTGGCAGGCCAACGCCAATAAAGCGCAGCTCGCTGATAAGGCCgct                                                                            >  2:97618/1‑144 (MQ=255)

                                                                        gccgtCGTGGGGCTGCTGTGAGCGTTGGGGCCACCCGCGTGGTCGCCGGGGCGGTGCTGCGGGCGGCCAGGGGGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACt                                                                        <  8:65619/143‑1 (MQ=255)

                                                                             cGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCCGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCgg                                                                    >  7:206982/1‑146 (MQ=255)

                                                                                  ggctgcAGTGCGCGCTGGGGCCCCCCGCCTGGGCGCCGTGGCGCGGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCa                                                              <  5:9649/146‑1 (MQ=255)

                                                                                       cAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTgg                                                         >  7:46178/1‑147 (MQ=255)

                                                                                        aGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGc                                                        >  7:77400/1‑147 (MQ=255)

                                                                                        aGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCGGGGTGTGGCAGGCCAACGCCGATAAGGCGCCGCTCGCTGGTCAGGCCGATGACTTCGGCAAGCAGTTggg                                                        >  7:202561/1‑146 (MQ=255)

                                                                                                  tGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAATCAGTTGGCGGAGAAGGAt                                              >  5:94512/1‑147 (MQ=255)

                                                                                                    ggCCACCCGCGGGGGCGCGGGGGCGGGGCGGCGGGCCGCCAGGGGGGGGGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATcg                                            <  6:188516/147‑1 (MQ=255)

                                                                                                              cTGGGCGCGGGGGCGCTGCGGCGGGCCGCCCGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGt                                  <  1:57021/147‑1 (MQ=255)

                                                                                                                  tCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCCGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAACCAATTGGCGGAGAAGGATCGCGCGCACGGTCt                                >  2:2390/1‑145 (MQ=255)

                                                                                                                      ggTGGCGCTGCTGCTGGCCGCCAGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCg                          <  5:237134/146‑1 (MQ=255)

                                                                                                                                 tgggggCCGCCCGGGGGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTg               <  2:75600/143‑1 (MQ=255)

                                                                                                                                  gctgGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCt                >  1:66921/1‑145 (MQ=255)

                                                                                                                                     ggCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTgca             >  7:223580/1‑145 (MQ=255)

                                                                                                                                          ccAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGcagcagcag      >  7:190009/1‑147 (MQ=255)

                                                                                                                                           cAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCagcagcagc     >  6:99598/1‑147 (MQ=255)

                                                                                                                                            aGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAgcg    >  5:181233/1‑147 (MQ=255)

                                                                                                                                              cgcTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCt  >  4:99878/1‑147 (MQ=255)

                                                                                                                                              cgcTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCt  >  5:129827/1‑147 (MQ=255)

ATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCT  >  NC_002947_CJ‑RC/3447146‑3447434

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A